# configuration file for GenBank/RefSeq alignment process
#
# $Id: genbank.conf,v 1.371 2010/05/28 17:59:39 chinhli Exp $
#

##
# cluster configuration
##

# swarm
cluster.rootDir = /hive/data/outside/genbank/build
cluster.paraHub = ku.gi.ucsc.edu

##
# only allow build on designated server
##
build.server = genbank

##
# Root where grepIndex files are build
##
grepIndex.rootDir = /data/tmp/grepIndex

##
# default values, which can be overridden for each genome
##

##
# Alignment genome partition window and overlap sizes.  Default values were
# chosen to balance number of jobs, average run time and longest jobs for
# human mRNA alignments.
##
default.align.window           =  80000000
default.align.overlap          =   3000000
default.align.maxGap           =   3000000
default.align.maxJobTargetSize =  80000000

##
# Minimum size of an unplaced seq to process, smaller sequences are skipped.
# Value suggested by Jim Kent. "logical place to cut off is 'contigs' that
# are composed of single reads, the single read size these days tends to be
# about 750.  So perhaps a cut off of 900."
default.align.minUnplacedSize = 900

##
# max size of query fasta files to create, in megabytes.
##
default.align.querySplitSize = 4

##
# pslCDnaFilter parameters variable definitions by genome assembly category,
# and type of cDNA sequence.
#
# The assembly categories are:
#   - finished - high quality
#   - ordered - well ordered, whole genome shotgun
#   - lowCover - low coverage (< 4x), lots of contigs, N50 scaffold size < 1mb
##

# common paramters used for all assembly categories
var.common.refseq.mrna.native.pslCDnaFilter  = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes
var.common.refseq.mrna.xeno.pslCDnaFilter    = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes
var.common.genbank.mrna.native.pslCDnaFilter = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes
var.common.genbank.mrna.xeno.pslCDnaFilter   = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes
var.common.genbank.est.native.pslCDnaFilter  = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes -usePolyTHead
var.common.genbank.est.xeno.pslCDnaFilter    = -minQSize=20 -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap -polyASizes -usePolyTHead

# common paramters used for local near best filtering
var.localNB.refseq.mrna.native.pslCDnaFilter  = -localNearBest=0.001 ${common.refseq.mrna.native.pslCDnaFilter}
var.localNB.refseq.mrna.xeno.pslCDnaFilter    = -localNearBest=0.010 ${common.refseq.mrna.xeno.pslCDnaFilter}
var.localNB.genbank.mrna.native.pslCDnaFilter = -localNearBest=0.005 ${common.genbank.mrna.native.pslCDnaFilter}
var.localNB.genbank.mrna.xeno.pslCDnaFilter   = -localNearBest=0.010 ${common.genbank.mrna.xeno.pslCDnaFilter}
var.localNB.genbank.est.native.pslCDnaFilter  = -localNearBest=0.005 ${common.genbank.est.native.pslCDnaFilter}
var.localNB.genbank.est.xeno.pslCDnaFilter    = -localNearBest=0.010 ${common.genbank.est.xeno.pslCDnaFilter}

# common paramters used for global near best filtering
var.globalNB.refseq.mrna.native.pslCDnaFilter  = -globalNearBest=0.0010  ${common.refseq.mrna.native.pslCDnaFilter}
var.globalNB.refseq.mrna.xeno.pslCDnaFilter    = -globalNearBest=0.0100  ${common.refseq.mrna.xeno.pslCDnaFilter}
var.globalNB.genbank.mrna.native.pslCDnaFilter = -globalNearBest=0.0025  ${common.genbank.mrna.native.pslCDnaFilter}
var.globalNB.genbank.mrna.xeno.pslCDnaFilter   = -globalNearBest=0.0100  ${common.genbank.mrna.xeno.pslCDnaFilter}
var.globalNB.genbank.est.native.pslCDnaFilter  = -globalNearBest=0.0025  ${common.genbank.est.native.pslCDnaFilter}
var.globalNB.genbank.est.xeno.pslCDnaFilter    = -globalNearBest=0.0100  ${common.genbank.est.xeno.pslCDnaFilter}

# finished assemblies
var.finished.refseq.mrna.native.pslCDnaFilter  = -minId=0.95 -minCover=0.25 ${globalNB.refseq.mrna.native.pslCDnaFilter}
var.finished.refseq.mrna.xeno.pslCDnaFilter    = -minId=0.35 -minCover=0.25 ${globalNB.refseq.mrna.xeno.pslCDnaFilter}
var.finished.genbank.mrna.native.pslCDnaFilter = -minId=0.95 -decayMinCover ${globalNB.genbank.mrna.native.pslCDnaFilter}
var.finished.genbank.mrna.xeno.pslCDnaFilter   = -minId=0.35 -minCover=0.25 ${globalNB.genbank.mrna.xeno.pslCDnaFilter}
var.finished.genbank.est.native.pslCDnaFilter  = -minId=0.95 -minCover=0.25 ${globalNB.genbank.est.native.pslCDnaFilter}
var.finished.genbank.est.xeno.pslCDnaFilter    = -minId=0.10 -minCover=0.10 ${globalNB.genbank.est.xeno.pslCDnaFilter}

# well-ordered assemblies
var.ordered.refseq.mrna.native.pslCDnaFilter  = -minId=0.95 -minCover=0.15 ${localNB.refseq.mrna.native.pslCDnaFilter}
var.ordered.refseq.mrna.xeno.pslCDnaFilter    = -minId=0.35 -minCover=0.15 ${localNB.refseq.mrna.xeno.pslCDnaFilter}
var.ordered.genbank.mrna.native.pslCDnaFilter = -minId=0.95 -minCover=0.15 ${localNB.genbank.mrna.native.pslCDnaFilter}
var.ordered.genbank.mrna.xeno.pslCDnaFilter   = -minId=0.35 -minCover=0.15 ${localNB.genbank.mrna.xeno.pslCDnaFilter}
var.ordered.genbank.est.native.pslCDnaFilter  = -minId=0.95 -minCover=0.15 ${localNB.genbank.est.native.pslCDnaFilter}
var.ordered.genbank.est.xeno.pslCDnaFilter    = -minId=0.35 -minCover=0.10 ${localNB.genbank.est.xeno.pslCDnaFilter}

# low-coverage assemblies
var.lowCover.refseq.mrna.native.pslCDnaFilter  = -minId=0.94 -minAlnSize=80 ${localNB.refseq.mrna.native.pslCDnaFilter}
var.lowCover.refseq.mrna.xeno.pslCDnaFilter    = -minId=0.33 -minAlnSize=80 ${localNB.refseq.mrna.xeno.pslCDnaFilter}
var.lowCover.genbank.mrna.native.pslCDnaFilter = -minId=0.94 -minAlnSize=80 ${localNB.genbank.mrna.native.pslCDnaFilter}
var.lowCover.genbank.mrna.xeno.pslCDnaFilter   = -minId=0.33 -minAlnSize=80 ${localNB.genbank.mrna.xeno.pslCDnaFilter}
var.lowCover.genbank.est.native.pslCDnaFilter  = -minId=0.94 -minAlnSize=50 ${localNB.genbank.est.native.pslCDnaFilter}
var.lowCover.genbank.est.xeno.pslCDnaFilter    = -minId=0.33 -minAlnSize=50 ${localNB.genbank.est.xeno.pslCDnaFilter}

default.perChromTables = yes

default.genbank.mrna.native.load = yes
default.genbank.mrna.native.loadDesc = yes

default.genbank.mrna.xeno.load = no
default.genbank.mrna.xeno.loadDesc = no

default.genbank.est.native.load = yes
default.genbank.est.native.loadDesc = no

default.genbank.est.xeno.load = no
default.genbank.est.xeno.loadDesc = no

default.refseq.mrna.native.load = yes
default.refseq.mrna.native.loadDesc = yes

default.refseq.mrna.xeno.load  = yes
default.refseq.mrna.xeno.loadDesc = yes

##
# genome configurations
##
# hg15test - used for debugging
hg15test.serverGenome = /hive/data/genomes/hg15/nib/chr*.nib
hg15test.ooc = /hive/data/genomes/hg15/11.ooc
hg15test.lift = /hive/data/genomes/hg15/jkStuff/liftAll.lft
#hg15test.align.unplacedChroms = chrUn_random
hg15test.align.unplacedChroms = chr*_random
hg15test.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
hg15test.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
hg15test.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
hg15test.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
hg15test.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
hg15test.mgc = yes
hg15test.orfeome = yes
hg15test.downloadDir = 10april1970
hg15test.genbank.mrna.blatTargetDb = yes
hg15test.refseq.mrna.blatTargetDb = yes


# hg16
hg16.serverGenome = /hive/data/genomes/hg16/hg16.2bit
hg16.ooc = /hive/data/genomes/hg16/11.ooc
hg16.lift = /hive/data/genomes/hg16/jkStuff/liftAll.lft
hg16.align.unplacedChroms = chrUn_random
hg16.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
hg16.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
hg16.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
hg16.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
hg16.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
hg16.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
hg16.genbank.est.xeno.load = yes
hg16.genbank.mrna.xeno.load  = yes
hg16.mgc = yes
hg16.upstreamGeneTbl = refGene
hg16.upstreamMaf = mzPt1Mm3Rn3Gg2_pHMM /hive/data/genomes/hg16/bed/multiz.hg16mm3rn3panTro1galGal2/species.lst

# hg17
hg17.serverGenome = /hive/data/genomes/hg17/hg17.2bit
hg17.ooc = /hive/data/genomes/hg17/11.ooc
hg17.lift = /hive/data/genomes/hg17/jkStuff/liftAll.lft
hg17.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
hg17.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
hg17.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
hg17.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
hg17.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
hg17.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
hg17.genbank.mrna.xeno.load  = yes
hg17.genbank.est.xeno.load = yes
hg17.refseq.mrna.xeno.load  = yes
hg17.refseq.mrna.xeno.loadDesc = yes
hg17.mgc = yes
hg17.orfeome = yes
hg17.downloadDir = hg17
hg17.upstreamGeneTbl = refGene
hg17.upstreamMaf = multiz17way /hive/data/genomes/hg17/bed/multiz17way/species.lst

# hg18
hg18.serverGenome = /hive/data/genomes/hg18/hg18.2bit
hg18.ooc = /hive/data/genomes/hg18/11.ooc
hg18.lift = /hive/data/genomes/hg18/jkStuff/liftAll.lft
hg18.hapRegions = /hive/data/genomes/hg18/bed/haplotypePos/haplotypePos.psl
hg18.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
hg18.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
hg18.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
hg18.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
hg18.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter}
hg18.genbank.est.xeno.pslCDnaFilter   = ${finished.genbank.est.xeno.pslCDnaFilter}
hg18.genbank.mrna.xeno.load  = yes
hg18.genbank.est.xeno.load = yes
hg18.refseq.mrna.xeno.load  = yes
hg18.refseq.mrna.xeno.loadDesc = yes
hg18.mgc = yes
hg18.orfeome = yes
hg18.downloadDir = hg18
hg18.ccds.buildId = 5
hg18.upstreamGeneTbl = refGene
hg18.upstreamMaf = multiz28way /hive/data/genomes/hg18/bed/multiz28way/species.lst multiz44way /hive/data/genomes/hg18/bed/multiz44way/species.list
hg18.genbank.mrna.blatTargetDb = yes


# braNey1 - GRCh37 - Genome Reference Consortium Human Reference 37
#       Assembly Accession: GCA_000001405.1
braNey1.serverGenome = /hive/data/genomes/hg19/hg19.2bit
braNey1.ooc = /hive/data/genomes/hg19/11.ooc
braNey1.lift = /hive/data/genomes/hg19/jkStuff/hg19.unBridged.lift
braNey1.hapRegions = /hive/data/genomes/hg19/jkStuff/hg19.haplotypes.psl
#braNey1.refseq.mrna.native.pslCDnaFilter  = -maxAlignsDrop=50 -ignoreIntrons -repsAsMatch ${finished.refseq.mrna.native.pslCDnaFilter}
braNey1.refseq.mrna.native.pslCDnaFilter  = -ignoreIntrons -repsAsMatch ${finished.refseq.mrna.native.pslCDnaFilter}
braNey1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
#braNey1.genbank.mrna.native.pslCDnaFilter = -maxAlignsDrop=50 -ignoreIntrons -repsAsMatch ${finished.genbank.mrna.native.pslCDnaFilter}
braNey1.genbank.mrna.native.pslCDnaFilter = -ignoreIntrons -repsAsMatch ${finished.genbank.mrna.native.pslCDnaFilter}
braNey1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
#braNey1.genbank.est.native.pslCDnaFilter = -maxAlignsDrop=50 -ignoreIntrons -repsAsMatch ${finished.genbank.est.native.pslCDnaFilter}
braNey1.genbank.est.native.pslCDnaFilter = -ignoreIntrons -repsAsMatch ${finished.genbank.est.native.pslCDnaFilter}
braNey1.genbank.est.xeno.pslCDnaFilter   = ${finished.genbank.est.xeno.pslCDnaFilter}
braNey1.genbank.mrna.xeno.load  = no
braNey1.genbank.est.xeno.load = no
braNey1.refseq.mrna.xeno.load  = yes
braNey1.refseq.mrna.xeno.loadDesc = yes
braNey1.mgc = yes
braNey1.orfeome = yes
braNey1.downloadDir = hg19
braNey1.upstreamGeneTbl = refGene
braNey1.upstreamMaf = multiz46way /hive/data/genomes/hg19/bed/multiz46way/species.list
braNey1.genbank.mrna.blatTargetDb = yes
braNey1.perChromTables = no
braNey1.addVersionToTables = yes

# braNey38 - GRCh38 - Genome Reference Consortium Human Reference 38
#       Assembly Accession: GCA_000001405.1
braNey38.serverGenome = /hive/data/genomes/hg38/hg38.2bit
braNey38.ooc = /hive/data/genomes/hg38/hg38.11.ooc
braNey38.lift = /hive/data/genomes/hg38/hg38.contigs.lift
braNey38.hapRegions = /hive/data/genomes/hg38/jkStuff/hg38.haplotypes.psl
braNey38.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
braNey38.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
braNey38.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
braNey38.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
braNey38.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter}
braNey38.genbank.est.xeno.pslCDnaFilter   = ${finished.genbank.est.xeno.pslCDnaFilter}
#braNey38.genbank.mrna.xeno.load  = yes
#braNey38.genbank.est.xeno.load = yes
braNey38.refseq.mrna.xeno.load  = yes
braNey38.refseq.mrna.xeno.loadDesc = yes
#braNey38.mgc = yes
#braNey38.orfeome = yes
#braNey38.downloadDir = hg38
braNey38.ccds.buildId = 20
# hg38.upstreamGeneTbl = refGene
# hg38.upstreamMaf = multiz46way /hive/data/genomes/hg38/bed/multiz46way/species.list
braNey38.genbank.mrna.blatTargetDb = yes
braNey38.perChromTables = no

# grcHhh38 - ANGIE TEST GRCh38 - Genome Reference Consortium Human Reference 38
#       Assembly Accession: GCA_000001405.1
grcHhh38.serverGenome = /hive/data/genomes/grcHhh38/grcHhh38.2bit
grcHhh38.ooc = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.11.ooc
grcHhh38.lift = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.contigs.lift
#grcHhh38.hapRegions = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.haplotypes.psl
#grcHhh38.hapRegions = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.p11.alt.psl
grcHhh38.hapRegions = /hive/data/genomes/grcHhh38/jkStuff/grcHhh38.p12.alt.psl
grcHhh38.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
grcHhh38.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
grcHhh38.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
grcHhh38.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
grcHhh38.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter}
grcHhh38.genbank.est.xeno.pslCDnaFilter   = ${finished.genbank.est.xeno.pslCDnaFilter}
#grcHhh38.genbank.mrna.xeno.load  = yes
#grcHhh38.genbank.est.xeno.load = yes
grcHhh38.refseq.mrna.xeno.load  = yes
grcHhh38.refseq.mrna.xeno.loadDesc = yes
#grcHhh38.mgc = yes
#grcHhh38.orfeome = yes
#grcHhh38.downloadDir = grcHhh38
#grcHhh38.ccds.buildId = 20
# grcHhh38.upstreamGeneTbl = refGene
# grcHhh38.upstreamMaf = multiz46way /hive/data/genomes/grcHhh38/bed/multiz46way/species.list
grcHhh38.genbank.mrna.blatTargetDb = yes
grcHhh38.perChromTables = no

# hg38 - GRCh38 - Genome Reference Consortium Human Reference 38
#       Assembly Accession: GCA_000001405.1
#       For now we want to keep the 2bit on p13 to avoid
#       re-annotating for each patch. In the future we can
#       bump the version when we selectively want to re-do
#       the alignment
hg38.serverGenome = /hive/data/genomes/hg38/hg38.p13.2bit
hg38.ooc = /hive/data/genomes/hg38/hg38.11.ooc
hg38.lift = /hive/data/genomes/hg38/hg38.contigs.lift
hg38.hapRegions = /hive/data/genomes/hg38/jkStuff/hg38.p13.alt.psl
hg38.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
hg38.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
hg38.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
hg38.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
hg38.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter}
hg38.genbank.est.xeno.pslCDnaFilter   = ${finished.genbank.est.xeno.pslCDnaFilter}
hg38.genbank.mrna.xeno.load  = yes
hg38.genbank.mrna.xeno.loadDesc = yes
hg38.genbank.est.xeno.load = yes
hg38.refseq.mrna.xeno.load  = yes
hg38.refseq.mrna.xeno.loadDesc = yes
hg38.mgc = yes
hg38.orfeome = yes
hg38.downloadDir = hg38
hg38.ccds.buildId = 20
hg38.upstreamGeneTbl = refGene
# hg38.upstreamMaf = multiz46way /hive/data/genomes/hg38/bed/multiz46way/species.list
hg38.genbank.mrna.blatTargetDb = yes
hg38.perChromTables = no

# hg19 - GRCh37 - Genome Reference Consortium Human Reference 37
#       Assembly Accession: GCA_000001405.1
#hg19.serverGenome = /hive/data/genomes/hg19/hg19.2bit
hg19.serverGenome = /hive/data/genomes/hg19/hg19.initial.2bit
hg19.ooc = /hive/data/genomes/hg19/11.ooc
hg19.lift = /hive/data/genomes/hg19/jkStuff/hg19.unBridged.lift
#hg19.hapRegions = /hive/data/genomes/hg19/jkStuff/hg19.p13.alt.psl
hg19.hapRegions = /hive/data/genomes/hg19/jkStuff/hg19.haplotypes.psl
hg19.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
hg19.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
hg19.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
hg19.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
hg19.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter}
hg19.genbank.est.xeno.pslCDnaFilter   = ${finished.genbank.est.xeno.pslCDnaFilter}
hg19.genbank.mrna.xeno.load  = yes
hg19.genbank.est.xeno.load = yes
hg19.refseq.mrna.xeno.load  = yes
hg19.refseq.mrna.xeno.loadDesc = yes
hg19.mgc = yes
hg19.orfeome = yes
hg19.downloadDir = hg19
hg19.ccds.buildId = 15
hg19.upstreamGeneTbl = refGene
hg19.upstreamMaf = multiz46way /hive/data/genomes/hg19/bed/multiz46way/species.list
hg19.genbank.mrna.blatTargetDb = yes
hg19.perChromTables = no

# CHM1 - alternative Human assembly
# refseq use less stringent filtering to annotate duplications
CHM1.serverGenome = /hive/data/genomes/CHM1/CHM1.2bit
CHM1.ooc = /hive/data/genomes/CHM1/11.ooc
CHM1.lift = /hive/data/genomes/CHM1/jkStuff/CHM1.unBridged.lift
CHM1.refseq.mrna.native.pslCDnaFilter = -minId=0.95 -minCover=0.25 -localNearBest=0.010 ${common.refseq.mrna.native.pslCDnaFilter}
CHM1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
CHM1.genbank.est.native.pslCDnaFilter = ${finished.genbank.est.native.pslCDnaFilter}
CHM1.genbank.mrna.native.load  = yes
CHM1.genbank.mrna.xeno.load  = no
CHM1.genbank.est.native.load = yes
CHM1.genbank.est.xeno.load = no
CHM1.refseq.mrna.native.load  = yes
CHM1.refseq.mrna.xeno.load  = no
CHM1.downloadDir = CHM1
CHM1.perChromTables = no

# regenCho1 (Cricetulus griseus - Chinese hamster ovary cell line CHO-K1)
regenCho1.serverGenome = /hive/data/genomes/regenCho1/regenCho1.2bit
regenCho1.ooc = /hive/data/genomes/regenCho1/jkStuff/regenCho1.11.ooc
regenCho1.lift = /hive/data/genomes/regenCho1/jkStuff/nonBridged.lift
regenCho1.downloadDir = regenCho1
regenCho1.perChromTables = no
regenCho1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
regenCho1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
regenCho1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
regenCho1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
regenCho1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# regenCho1.upstreamGeneTbl = ensGene
# regenCho1.upstreamMaf = multiz9way /hive/data/genomes/regenCho1/bed/multiz9way/species.list

# criGriChoV2 (Cricetulus griseus - Chinese hamster ovary cell line CHO-K1)
criGriChoV2.serverGenome = /hive/data/genomes/criGriChoV2/criGriChoV2.2bit
criGriChoV2.ooc = /hive/data/genomes/criGriChoV2/jkStuff/criGriChoV2.11.ooc
criGriChoV2.lift = no
criGriChoV2.downloadDir = criGriChoV2
criGriChoV2.perChromTables = no
criGriChoV2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
criGriChoV2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
criGriChoV2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
criGriChoV2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
criGriChoV2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# criGriChoV2.upstreamGeneTbl = ensGene
# criGriChoV2.upstreamMaf = multiz9way /hive/data/genomes/criGriChoV2/bed/multiz9way/species.list

# criGriChoV1 (Cricetulus griseus - Chinese hamster ovary cell line CHO-K1)
criGriChoV1.serverGenome = /hive/data/genomes/criGriChoV1/criGriChoV1.2bit
criGriChoV1.ooc = /hive/data/genomes/criGriChoV1/jkStuff/criGriChoV1.11.ooc
criGriChoV1.lift = no
criGriChoV1.downloadDir = criGriChoV1
criGriChoV1.perChromTables = no
criGriChoV1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
criGriChoV1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
criGriChoV1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
criGriChoV1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
criGriChoV1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# criGriChoV1.upstreamGeneTbl = ensGene
# criGriChoV1.upstreamMaf = multiz9way /hive/data/genomes/criGriChoV1/bed/multiz9way/species.list

# criGri1 (Chinese hamster)
criGri1.serverGenome = /hive/data/genomes/criGri1/criGri1.2bit
criGri1.ooc = /hive/data/genomes/criGri1/jkStuff/criGri1.11.ooc
criGri1.lift = no
criGri1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
criGri1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
criGri1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
criGri1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
criGri1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
criGri1.refseq.mrna.native.load = yes
criGri1.refseq.mrna.xeno.load = yes
criGri1.genbank.mrna.xeno.load = no
criGri1.genbank.est.native.load = yes
criGri1.genbank.mrna.native.load = yes
criGri1.genbank.mrna.native.loadDesc = no
criGri1.downloadDir = criGri1
criGri1.perChromTables = no

# aotNan1 (Ma's night monkey / Aotus nancymaae / taxId 37293)
aotNan1.serverGenome = /hive/data/genomes/aotNan1/aotNan1.2bit
aotNan1.ooc = /hive/data/genomes/aotNan1/jkStuff/aotNan1.11.ooc
aotNan1.lift = no
aotNan1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
aotNan1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
aotNan1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
aotNan1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
aotNan1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
aotNan1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
aotNan1.downloadDir = aotNan1
aotNan1.refseq.mrna.native.load  = yes
aotNan1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
aotNan1.genbank.mrna.xeno.load = no
aotNan1.genbank.mrna.native.load = no
aotNan1.genbank.est.native.load = no
aotNan1.perChromTables = no

# cebCap1 (White-faced sapajou - Cebus capucinus imitator) taxId 1737458
cebCap1.serverGenome = /hive/data/genomes/cebCap1/cebCap1.2bit
cebCap1.ooc = /hive/data/genomes/cebCap1/jkStuff/cebCap1.11.ooc
cebCap1.lift = no
cebCap1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
cebCap1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
cebCap1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
cebCap1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
cebCap1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
cebCap1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
cebCap1.downloadDir = cebCap1
cebCap1.refseq.mrna.native.load  = yes
cebCap1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
cebCap1.genbank.mrna.xeno.load = no
cebCap1.genbank.mrna.native.load = no
cebCap1.genbank.est.native.load = no
cebCap1.perChromTables = no

# cerAty1 (Sooty mangabey - Cercocebus atys) taxId 9531
cerAty1.serverGenome = /hive/data/genomes/cerAty1/cerAty1.2bit
cerAty1.ooc = /hive/data/genomes/cerAty1/jkStuff/cerAty1.11.ooc
cerAty1.lift = no
cerAty1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
cerAty1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
cerAty1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
cerAty1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
cerAty1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
cerAty1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
cerAty1.downloadDir = cerAty1
cerAty1.refseq.mrna.native.load  = yes
cerAty1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
cerAty1.genbank.mrna.xeno.load = no
cerAty1.genbank.mrna.native.load = no
cerAty1.genbank.est.native.load = no
cerAty1.perChromTables = no

# manLeu1 (Drill - Mandrillus leucophaeus) taxId 9568
manLeu1.serverGenome = /hive/data/genomes/manLeu1/manLeu1.2bit
manLeu1.ooc = /hive/data/genomes/manLeu1/jkStuff/manLeu1.11.ooc
manLeu1.lift = no
manLeu1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
manLeu1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
manLeu1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
manLeu1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
manLeu1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
manLeu1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
manLeu1.downloadDir = manLeu1
manLeu1.refseq.mrna.native.load  = yes
manLeu1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
manLeu1.genbank.mrna.xeno.load = no
manLeu1.genbank.mrna.native.load = no
manLeu1.genbank.est.native.load = no
manLeu1.perChromTables = no

# neoSch1 (Hawaiian monk seal - Neomonachus schauinslandi) taxId 29088
neoSch1.serverGenome = /hive/data/genomes/neoSch1/neoSch1.2bit
neoSch1.ooc = /hive/data/genomes/neoSch1/jkStuff/neoSch1.11.ooc
neoSch1.lift = no
neoSch1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
neoSch1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
neoSch1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
neoSch1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
neoSch1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
neoSch1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
neoSch1.downloadDir = neoSch1
neoSch1.refseq.mrna.native.load  = no
neoSch1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
neoSch1.genbank.mrna.xeno.load = no
neoSch1.genbank.mrna.native.load = no
neoSch1.genbank.est.native.load = no
neoSch1.perChromTables = no

# proCoq1 (Coquerel's sifaka - Propithecus coquereli) taxId 379532
proCoq1.serverGenome = /hive/data/genomes/proCoq1/proCoq1.2bit
proCoq1.ooc = /hive/data/genomes/proCoq1/jkStuff/proCoq1.11.ooc
proCoq1.lift = no
proCoq1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
proCoq1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
proCoq1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
proCoq1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
proCoq1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
proCoq1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
proCoq1.downloadDir = proCoq1
proCoq1.refseq.mrna.native.load  = yes
proCoq1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
proCoq1.genbank.mrna.xeno.load = no
proCoq1.genbank.mrna.native.load = no
proCoq1.genbank.est.native.load = no
proCoq1.perChromTables = no

# mm7
mm7.serverGenome = /hive/data/genomes/mm7/mm7.2bit
mm7.ooc = /hive/data/genomes/mm7/11.ooc
mm7.align.unplacedChroms = chrUn_random
mm7.lift = /hive/data/genomes/mm7/jkStuff/liftAll.lft
mm7.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
mm7.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
mm7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
mm7.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
mm7.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
mm7.downloadDir = mm7
mm7.refseq.mrna.xeno.load  = yes
mm7.refseq.mrna.xeno.loadDesc = yes
mm7.genbank.mrna.xeno.load  = yes
mm7.mgc = yes
mm7.upstreamGeneTbl = refGene
mm7.upstreamMaf = multiz17way /hive/data/genomes/mm7/bed/multiz17way/species.lst

# mm8
mm8.serverGenome = /hive/data/genomes/mm8/mm8.2bit
mm8.ooc = /hive/data/genomes/mm8/11.ooc
mm8.align.unplacedChroms = chrUn_random
mm8.lift = /hive/data/genomes/mm8/jkStuff/liftAll.lft
mm8.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
mm8.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
mm8.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
mm8.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
mm8.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
mm8.downloadDir = mm8
mm8.refseq.mrna.xeno.load  = yes
mm8.refseq.mrna.xeno.loadDesc = yes
mm8.genbank.mrna.xeno.load  = yes
mm8.mgc = yes
mm8.upstreamGeneTbl = refGene
mm8.upstreamMaf = multiz17way /hive/data/genomes/mm8/bed/multiz17way/species.lst

# mm9
mm9.serverGenome = /hive/data/genomes/mm9/mm9.2bit
mm9.ooc = /hive/data/genomes/mm9/11.ooc
mm9.align.unplacedChroms = *_random
mm9.lift = /hive/data/genomes/mm9/jkStuff/nonBridgedGap.lft
mm9.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
mm9.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
mm9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
mm9.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
mm9.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
mm9.downloadDir = mm9
mm9.refseq.mrna.xeno.load  = yes
mm9.refseq.mrna.xeno.loadDesc = yes
mm9.genbank.mrna.xeno.load  = yes
mm9.mgc = yes
mm9.orfeome = yes
mm9.ccds.buildId = 7
mm9.upstreamGeneTbl = refGene
mm9.upstreamMaf = multiz30way /hive/data/genomes/mm9/bed/multiz30way/species.list
mm9.genbank.mrna.blatTargetDb = yes

# GRCm38B
GRCm38B.serverGenome = /hive/data/genomes/GRCm38B/GRCm38B.2bit
GRCm38B.ooc = /hive/data/genomes/GRCm38B/jkStuff/GRCm38B.11.ooc
GRCm38B.lift = /hive/data/genomes/GRCm38B/jkStuff/GRCm38B.nonBridged.lft
GRCm38B.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
GRCm38B.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
GRCm38B.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
GRCm38B.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
GRCm38B.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
GRCm38B.downloadDir = GRCm38B
GRCm38B.refseq.mrna.xeno.load  = yes
GRCm38B.refseq.mrna.xeno.loadDesc = yes
GRCm38B.genbank.mrna.xeno.load  = yes
#GRCm38B.mgc = yes
#GRCm38B.orfeome = yes
#GRCm38B.ccds.buildId = 21
#GRCm38B.genbank.mrna.blatTargetDb = yes
# GRCm38B.upstreamGeneTbl = refGene
# GRCm38B.upstreamMaf = multiz60way /hive/data/genomes/GRCm38B/bed/multiz60way/species.list

# mm39 - (house mouse - GCA_000001635.9 - GRCm39)
mm39.serverGenome = /hive/data/genomes/mm39/mm39.2bit
mm39.ooc = /hive/data/genomes/mm39/jkStuff/mm39.11.ooc
mm39.lift = /hive/data/genomes/mm39/jkStuff/mm39.5Kgaps.lft
mm39.perChromTables = no
mm39.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
mm39.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
mm39.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
mm39.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
mm39.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
mm39.downloadDir = mm39
mm39.refseq.mrna.xeno.load  = yes
mm39.refseq.mrna.xeno.loadDesc = yes
mm39.genbank.mrna.xeno.load  = yes
mm39.genbank.mrna.blatTargetDb = yes
mm39.upstreamGeneTbl = refGene
# mm39.mgc = yes
# mm39.orfeome = yes
# mm39.ccds.buildId = 21
# mm39.upstreamMaf = multiz60way /hive/data/genomes/mm39/bed/multiz60way/species.list

# mm10
mm10.serverGenome = /hive/data/genomes/mm10/mm10.2bit
mm10.ooc = /hive/data/genomes/mm10/mm10.11.ooc
mm10.lift = /hive/data/genomes/mm10/mm10.nonBridged.lift
mm10.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
mm10.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
mm10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
mm10.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
mm10.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
mm10.downloadDir = mm10
mm10.refseq.mrna.xeno.load  = yes
mm10.refseq.mrna.xeno.loadDesc = yes
mm10.genbank.mrna.xeno.load  = yes
mm10.mgc = yes
mm10.orfeome = yes
mm10.ccds.buildId = 21
mm10.genbank.mrna.blatTargetDb = yes
mm10.upstreamGeneTbl = refGene
mm10.upstreamMaf = multiz60way /hive/data/genomes/mm10/bed/multiz60way/species.list

# rn3
rn3.serverGenome = /hive/data/genomes/rn3/rn3.2bit
rn3.ooc = /hive/data/genomes/rn3/11.ooc
rn3.align.unplacedChroms = chrUn,chrUn_random
rn3.lift = /hive/data/genomes/rn3/jkStuff/liftAll.lft
rn3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
rn3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
rn3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
rn3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
rn3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
rn3.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
#rn3.genbank.mrna.xeno.load  = yes
rn3.downloadDir = rnJun2003
rn3.refseq.mrna.xeno.load = yes
rn3.mgc = yes
rn3.upstreamGeneTbl = refGene


# rn4
rn4.serverGenome = /hive/data/genomes/rn4/rn4.2bit
rn4.ooc = /hive/data/genomes/rn4/11.ooc
rn4.align.unplacedChroms = chrUn,chr*_random
rn4.lift = /hive/data/genomes/rn4/jkStuff/liftAll.lft
rn4.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
rn4.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
rn4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
rn4.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
rn4.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
rn4.downloadDir = rn4
rn4.refseq.mrna.xeno.load  = yes
rn4.refseq.mrna.xeno.loadDesc = yes
rn4.genbank.mrna.xeno.load  = yes
rn4.mgc = yes
rn4.upstreamGeneTbl = refGene
rn4.upstreamMaf = multiz9way /hive/data/genomes/rn4/bed/multiz9way/species.lst

# rn5 (rat)
rn5.serverGenome = /hive/data/genomes/rn5/rn5.2bit
rn5.ooc = /hive/data/genomes/rn5/jkStuff/rn5.11.ooc
rn5.lift = /hive/data/genomes/rn5/jkStuff/rn5.nonBridged.lift
rn5.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
rn5.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
rn5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
rn5.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
rn5.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
rn5.downloadDir = rn5
rn5.refseq.mrna.xeno.load  = yes
rn5.refseq.mrna.xeno.loadDesc = yes
rn5.genbank.mrna.xeno.load  = yes
rn5.perChromTables = no
rn5.mgc = yes
rn5.upstreamGeneTbl = ensGene
rn5.upstreamMaf = multiz13way /hive/data/genomes/rn5/bed/multiz13way/species.list.txt

# regenRn1 (Regeneron rat assembly)
regenRn1.serverGenome = /hive/data/genomes/regenRn1/regenRn1.2bit
regenRn1.ooc = /hive/data/genomes/regenRn1/jkStuff/regenRn1.11.ooc
regenRn1.lift = /hive/data/genomes/regenRn1/jkStuff/nonBridged.lift
regenRn1.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
regenRn1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
regenRn1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
regenRn1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
regenRn1.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
regenRn1.downloadDir = regenRn1
regenRn1.refseq.mrna.xeno.load  = yes
regenRn1.refseq.mrna.xeno.loadDesc = yes
regenRn1.genbank.mrna.xeno.load  = yes
regenRn1.perChromTables = no
regenRn1.mgc = yes
# regenRn1.upstreamGeneTbl = ensGene
# regenRn1.upstreamMaf = multiz13way /hive/data/genomes/regenRn1/bed/multiz13way/species.list.txt

# regenRn0 (Regeneron rat assembly)
regenRn0.serverGenome = /hive/data/genomes/regenRn0/regenRn0.2bit
regenRn0.ooc = /hive/data/genomes/regenRn0/jkStuff/regenRn0.11.ooc
regenRn0.lift = /hive/data/genomes/regenRn0/jkStuff/nonBridged.lift
regenRn0.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
regenRn0.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
regenRn0.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
regenRn0.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
regenRn0.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
regenRn0.downloadDir = regenRn0
regenRn0.refseq.mrna.xeno.load  = yes
regenRn0.refseq.mrna.xeno.loadDesc = yes
regenRn0.genbank.mrna.xeno.load  = yes
regenRn0.perChromTables = no
regenRn0.mgc = yes
# regenRn0.upstreamGeneTbl = ensGene
# regenRn0.upstreamMaf = multiz13way /hive/data/genomes/regenRn0/bed/multiz13way/species.list.txt

# rn7 (rat GCF_015227675.2 mRatBN7.2)
rn7.serverGenome = /hive/data/genomes/rn7/rn7.2bit
rn7.ooc = /hive/data/genomes/rn7/jkStuff/rn7.11.ooc
rn7.lift = /hive/data/genomes/rn7/jkStuff/rn7.gaps.lft
rn7.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
rn7.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
rn7.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
rn7.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
rn7.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
rn7.downloadDir = rn7
rn7.refseq.mrna.xeno.load  = yes
rn7.refseq.mrna.xeno.loadDesc = yes
rn7.genbank.mrna.xeno.load  = yes
rn7.perChromTables = no
rn7.mgc = yes
# rn7.upstreamGeneTbl = ensGene
# rn7.upstreamMaf = multiz13way /hive/data/genomes/rn7/bed/multiz13way/species.list.txt

# rn6 (rat)
rn6.serverGenome = /hive/data/genomes/rn6/rn6.2bit
rn6.ooc = /hive/data/genomes/rn6/jkStuff/rn6.11.ooc
rn6.lift = /hive/data/genomes/rn6/jkStuff/rn6.nonBridged.lift
rn6.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
rn6.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
rn6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
rn6.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
rn6.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
rn6.downloadDir = rn6
rn6.refseq.mrna.xeno.load  = yes
rn6.refseq.mrna.xeno.loadDesc = yes
rn6.genbank.mrna.xeno.load  = yes
rn6.perChromTables = no
rn6.mgc = yes
# rn6.upstreamGeneTbl = ensGene
# rn6.upstreamMaf = multiz13way /hive/data/genomes/rn6/bed/multiz13way/species.list.txt

# micOch1 (prairie vole)
micOch1.serverGenome = /hive/data/genomes/micOch1/micOch1.2bit
micOch1.ooc = /hive/data/genomes/micOch1/jkStuff/micOch1.11.ooc
micOch1.lift = /hive/data/genomes/micOch1/jkStuff/nonBridged.lft
micOch1.perChromTables = no
micOch1.downloadDir = micOch1
micOch1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
micOch1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
micOch1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
micOch1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
micOch1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults are fine: genbank.mrna.native refseq.mrna.native refseq.mrna.xeno yes
# and genbank.est.native
# there is no multiple alignment yet:
# micOch1.upstreamGeneTbl = refGene
# micOch1.upstreamMaf = multiz7way
# /hive/data/genomes/micOch1/bed/multiz7way/species.lst

# fukDam1 - Fukomys damarensis (Damara mole-rat)
fukDam1.serverGenome = /hive/data/genomes/fukDam1/fukDam1.2bit
fukDam1.ooc = /hive/data/fukDam1/jkStuff/fukDam1.11.ooc
fukDam1.lift = no
fukDam1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
fukDam1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
fukDam1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
fukDam1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
fukDam1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
fukDam1.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
fukDam1.refseq.mrna.native.load  = yes
fukDam1.refseq.mrna.xeno.load = yes
fukDam1.genbank.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
fukDam1.genbank.mrna.xeno.load = yes
fukDam1.genbank.est.native.load = no
fukDam1.downloadDir = fukDam1
fukDam1.perChromTables = no

# hetGla2 (moleRat)
hetGla2.serverGenome = /hive/data/genomes/hetGla2/hetGla2.2bit
hetGla2.ooc = /hive/data/hetGla2/jkStuff/hetGla2.11.ooc
hetGla2.lift = no
hetGla2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
hetGla2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
hetGla2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
hetGla2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
hetGla2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
hetGla2.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
hetGla2.refseq.mrna.native.load  = no
hetGla2.refseq.mrna.xeno.load = yes
hetGla2.genbank.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
hetGla2.genbank.mrna.xeno.load = yes
hetGla2.genbank.est.native.load = no
hetGla2.downloadDir = hetGla2
hetGla2.perChromTables = no

# hetGla1 (moleRat)
hetGla1.serverGenome = /hive/data/genomes/hetGla1/hetGla1.2bit
hetGla1.ooc = /hive/data/genomes/hetGla1/hetGla1.11.ooc
hetGla1.lift = no
hetGla1.perChromTables = no
hetGla1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
hetGla1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
hetGla1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
hetGla1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
hetGla1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
hetGla1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
hetGla1.downloadDir = hetGla1
hetGla1.refseq.mrna.native.load  = no
hetGla1.refseq.mrna.xeno.load = yes
hetGla1.refseq.mrna.xeno.loadDesc  = yes
hetGla1.genbank.mrna.native.load = yes
hetGla1.genbank.mrna.native.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
hetGla1.genbank.mrna.xeno.load = yes
hetGla1.genbank.mrna.xeno.loadDesc = yes
hetGla1.genbank.est.native.load = yes
hetGla1.genbank.est.native.loadDesc = yes

# sarHar1 (Tasmanian Devil)
sarHar1.serverGenome = /hive/data/genomes/sarHar1/sarHar1.2bit
sarHar1.ooc = /hive/data/genomes/sarHar1/sarHar1.11.ooc
sarHar1.lift = no
sarHar1.perChromTables = no
sarHar1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
sarHar1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
sarHar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
sarHar1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
sarHar1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
sarHar1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
sarHar1.downloadDir = sarHar1
sarHar1.refSeq.native.load  = no
sarHar1.refseq.mrna.xeno.load = yes
sarHar1.refseq.mrna.xeno.loadDesc  = yes
sarHar1.genbank.mrna.native.load = yes
sarHar1.genbank.mrna.native.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
sarHar1.genbank.est.native.load = no
sarHar1.genbank.est.native.loadDesc = no

# fr1
fr1.serverGenome = /hive/data/genomes/fr1/fr1.2bit
fr1.ooc = no
fr1.align.unplacedChroms = chrUn
fr1.lift = /hive/data/genomes/fr1/Un/chrUn-frag.lft
fr1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
fr1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
fr1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
fr1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
fr1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
fr1.genbank.mrna.xeno.loadDesc = yes
fr1.refseq.mrna.native.load = no
fr1.refseq.mrna.xeno.load  = no
fr1.upstreamGeneTbl = ensGene

# fr2
fr2.serverGenome = /hive/data/genomes/fr2/fr2.2bit
fr2.ooc = /hive/data/genomes/fr2/11.ooc
fr2.align.unplacedChroms = chrUn
fr2.lift = /hive/data/genomes/fr2/jkStuff/liftAll.lft
fr2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
fr2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
fr2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
fr2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
fr2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
fr2.genbank.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
fr2.genbank.mrna.xeno.load = yes
fr2.refseq.mrna.native.load = no
fr2.refseq.mrna.xeno.load  = no
fr2.upstreamGeneTbl = ensGene
fr2.upstreamMaf = multiz5way /hive/data/genomes/fr2/bed/multiz5way/species.lst

# fr3
fr3.serverGenome = /hive/data/genomes/fr3/fr3.2bit
fr3.ooc = /hive/data/genomes/fr3/fr3.11.ooc
# fr3.lift = /hive/data/genomes/fr3/fr3.nonBridged.lift
fr3.perChromTables = no
fr3.lift = no
fr3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
fr3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
fr3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
fr3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
fr3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
fr3.genbank.mrna.xeno.loadDesc = yes
fr3.refseq.mrna.xeno.load  = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
fr3.genbank.mrna.xeno.load = yes
fr3.upstreamGeneTbl = ensGene
fr3.upstreamMaf = multiz8way /hive/data/genomes/fr3/bed/multiz8way/species.list

# dm1
dm1.serverGenome = /hive/data/genomes/dm1/nib/chr*.nib
dm1.ooc = /hive/data/genomes/dm1/11.ooc
dm1.lift = /hive/data/genomes/dm1/jkStuff/liftAll.lft
dm1.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
dm1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
dm1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
dm1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
dm1.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dm1.downloadDir = dm1

# dm2 (D. melanogaster)
dm2.serverGenome = /hive/data/genomes/dm2/nib/chr*.nib
dm2.ooc = /hive/data/genomes/dm1/11.ooc
dm2.lift = /hive/data/genomes/dm2/jkStuff/liftAll.lft
dm2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
dm2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
dm2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
dm2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
dm2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dm2.genbank.mrna.xeno.load = yes
dm2.downloadDir = dm2
dm2.upstreamGeneTbl = refGene
dm2.upstreamMaf = multiz15way /hive/data/genomes/dm2/bed/multiz15way/species.lst

# dm6 (D. melanogaster)
dm6.serverGenome = /hive/data/genomes/dm6/dm6.2bit
dm6.ooc = /hive/data/genomes/dm6/jkStuff/dm6.11.ooc
dm6.lift = no
dm6.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
dm6.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
dm6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
dm6.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
dm6.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dm6.genbank.mrna.xeno.load = yes
dm6.perChromTables = no
dm6.upstreamGeneTbl = refGene
dm6.upstreamMaf = multiz27way /hive/data/genomes/dm6/bed/multiz27way/species.list.txt

# dm3 (D. melanogaster)
dm3.serverGenome = /hive/data/genomes/dm3/dm3.2bit
dm3.ooc = /hive/data/genomes/dm3/11.ooc
dm3.lift = /hive/data/genomes/dm3/jkStuff/liftAll.lft
dm3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
dm3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
dm3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
dm3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
dm3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dm3.genbank.mrna.xeno.load = yes
dm3.upstreamGeneTbl = refGene
dm3.upstreamMaf = multiz15way /hive/data/genomes/dm3/bed/multiz15way/species.lst

# sacCer3 S. cerevisiae
sacCer3.serverGenome = /hive/data/genomes/sacCer3/sacCer3.2bit
sacCer3.ooc = no
sacCer3.maxIntron = 5000
sacCer3.lift = no
sacCer3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
sacCer3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
sacCer3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
sacCer3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
sacCer3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
#sacCer3.perChromTables = no  # doesn't work in the browser
sacCer3.genbank.mrna.xeno.load = no
sacCer3.refseq.mrna.native.load = no
sacCer3.downloadDir = sacCer3
sacCer3.upstreamGeneTbl = xenoRefGene
sacCer3.upstreamMaf = multiz7way /hive/data/genomes/sacCer3/bed/multiz7way/species.lst

# sacCer2 S. cerevisiae
sacCer2.serverGenome = /hive/data/genomes/sacCer2/sacCer2.2bit
sacCer2.ooc = no
sacCer2.maxIntron = 5000
sacCer2.lift = no
sacCer2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
sacCer2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
sacCer2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
sacCer2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
sacCer2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
#sacCer2.perChromTables = no  # doesn't work in the browser
sacCer2.genbank.mrna.xeno.load = no
sacCer2.refseq.mrna.native.load = no
sacCer2.downloadDir = sacCer2
sacCer2.upstreamGeneTbl = xenoRefGene
sacCer2.upstreamMaf = multiz7way /hive/data/genomes/sacCer2/bed/multiz7way/species.list

# sacCer1
sacCer1.serverGenome = /hive/data/genomes/sacCer1/nib/chr*.nib
sacCer1.ooc = no
sacCer1.maxIntron = 5000
sacCer1.lift = no
sacCer1.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
sacCer1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
sacCer1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
sacCer1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
sacCer1.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
#sacCer1.perChromTables = no  # doesn't work in the browser
sacCer1.genbank.mrna.xeno.load = no
sacCer1.refseq.mrna.native.load = no
sacCer1.downloadDir = sacCer1

# panPan3 (bonobo - Pan paniscus - GCF_013052645.1 Mhudiblu_PPA_v0 15 May 2020)
panPan3.serverGenome = /hive/data/genomes/panPan3/panPan3.2bit
panPan3.ooc = /hive/data/genomes/panPan3/jkStuff/panPan3.11.ooc
panPan3.lift = /hive/data/genomes/panPan3/jkStuff/panPan3.nonBridged.lft
panPan3.perChromTables = no
panPan3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
panPan3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
panPan3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
panPan3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
panPan3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
panPan3.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
panPan3.downloadDir = panPan3
# defaults yes genbank.mrna.native, genbank.est.native.load,
#              refseq.mrna.native, refseq.mrna.xeno
# DO NOT NEED genbank.mrna.xeno except for human, mouse
panPan3.genbank.est.native.load = no

# panPan2 (bonobo - Pan paniscus)
panPan2.serverGenome = /hive/data/genomes/panPan2/panPan2.2bit
panPan2.ooc = /hive/data/genomes/panPan2/jkStuff/panPan2.11.ooc
panPan2.lift = /hive/data/genomes/panPan2/jkStuff/panPan2.nonBridged.lft
panPan2.perChromTables = no
panPan2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
panPan2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
panPan2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
panPan2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
panPan2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
panPan2.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
panPan2.downloadDir = panPan2
# defaults yes genbank.mrna.native, genbank.est.native.load,
#              refseq.mrna.native, refseq.mrna.xeno
# DO NOT NEED genbank.mrna.xeno except for human, mouse
panPan2.genbank.est.native.load = no


# panPan1 (bonobo)
panPan1.serverGenome = /hive/data/genomes/panPan1/panPan1.2bit
panPan1.ooc = /hive/data/genomes/panPan1/jkStuff/panPan1.11.ooc
panPan1.lift = no
panPan1.perChromTables = no
panPan1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
panPan1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
panPan1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
panPan1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
panPan1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
panPan1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
panPan1.downloadDir = panPan1
panPan1.refseq.mrna.native.load = yes
panPan1.refseq.mrna.native.loadDesc = yes
panPan1.refseq.mrna.xeno.load  = yes
panPan1.refseq.mrna.xeno.loadDesc = yes
panPan1.genbank.mrna.native.load = yes
panPan1.genbank.mrna.native.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
panPan1.genbank.mrna.xeno.load = no
panPan1.genbank.est.native.load = no

# panTro6 (chimp - Pan troglodytes - refseq GCF_002880755.1 - taxId 9598)
panTro6.serverGenome = /hive/data/genomes/panTro6/panTro6.2bit
panTro6.ooc = /hive/data/genomes/panTro6/jkStuff/panTro6.11.ooc
panTro6.lift = /hive/data/genomes/panTro6/jkStuff/panTro6.nonBridged.lft
panTro6.perChromTables = no
panTro6.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
panTro6.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
panTro6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
panTro6.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
panTro6.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
panTro6.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
panTro6.downloadDir = panTro6
# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
# yes: genbank.est.native.load refseq.mrna.native.load
# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
# yes: refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
# no: genbank.est.native.loadDesc genbank.est.xeno.load
# no: genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# have been doing this for chimp too:
panTro6.genbank.mrna.xeno.load = yes

# panTro5 (chimp)
panTro5.serverGenome = /hive/data/genomes/panTro5/panTro5.2bit
panTro5.ooc = /hive/data/genomes/panTro5/jkStuff/panTro5.11.ooc
panTro5.lift = /hive/data/genomes/panTro5/jkStuff/nonBridged.lft
panTro5.perChromTables = no
panTro5.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
panTro5.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
panTro5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
panTro5.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
panTro5.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
panTro5.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
panTro5.downloadDir = panTro5
panTro5.refseq.mrna.native.load  = yes
panTro5.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
panTro5.genbank.mrna.xeno.load = yes
# panTro5.upstreamGeneTbl = ensGene
# panTro5.upstreamMaf = multiz12way /hive/data/genomes/panTro5/bed/multiz12way/species.list

# panTro4 (chimp)
panTro4.serverGenome = /hive/data/genomes/panTro4/panTro4.2bit
panTro4.ooc = /hive/data/genomes/panTro4/jkStuff/panTro4.11.ooc
panTro4.lift = /hive/data/genomes/panTro4/jkStuff/panTro4.nonBridged.lift
panTro4.perChromTables = no
panTro4.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
panTro4.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
panTro4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
panTro4.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
panTro4.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
panTro4.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
panTro4.downloadDir = panTro4
panTro4.refseq.mrna.native.load  = yes
panTro4.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
panTro4.genbank.mrna.xeno.load = yes
panTro4.genbank.mrna.xeno.loadDesc = yes
panTro4.genbank.est.native.load = yes
# panTro4.upstreamGeneTbl = ensGene
# panTro4.upstreamMaf = multiz12way /hive/data/genomes/panTro4/bed/multiz12way/species.list

# chimp
panTro3.serverGenome = /hive/data/genomes/panTro3/panTro3.2bit
panTro3.ooc = /hive/data/genomes/panTro3/panTro3.11.ooc
panTro3.align.unplacedChroms = chrUn*,chr*_random
panTro3.lift = /hive/data/genomes/panTro3/panTro3.nonBridged.lft
panTro3.perChromTables = no
panTro3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
panTro3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
panTro3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
panTro3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
panTro3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
panTro3.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
panTro3.downloadDir = panTro3
panTro3.refseq.mrna.native.load  = yes
panTro3.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
panTro3.genbank.mrna.xeno.load = yes
panTro3.genbank.mrna.xeno.loadDesc = yes
panTro3.genbank.est.native.load = yes
panTro3.upstreamGeneTbl = ensGene
panTro3.upstreamMaf = multiz12way /hive/data/genomes/panTro3/bed/multiz12way/species.list

panTro1.serverGenome = /hive/data/genomes/panTro1/panTro1.2bit
panTro1.ooc = /hive/data/genomes/panTro1/11.ooc
panTro1.align.unplacedChroms = chrUn_random
panTro1.lift = /hive/data/genomes/panTro1/jkStuff/liftAll.lft
panTro1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
panTro1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
panTro1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
panTro1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
panTro1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
panTro1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
panTro1.downloadDir = panTro1
panTro1.refseq.mrna.native.load  = yes
panTro1.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
panTro1.genbank.est.native.load = yes
panTro1.upstreamGeneTbl = ensGene

panTro2.serverGenome = /hive/data/genomes/panTro2/panTro2.2bit
panTro2.ooc = /hive/data/genomes/panTro2/11.ooc
panTro2.align.unplacedChroms = chrUn,chr*_random
panTro2.lift = /hive/data/genomes/panTro2/lifts/genbank.lft
panTro2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
panTro2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
panTro2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
panTro2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
panTro2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
panTro2.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
panTro2.downloadDir = panTro2
panTro2.refseq.mrna.native.load  = yes
panTro2.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
panTro2.genbank.mrna.xeno.load = yes
panTro2.genbank.mrna.xeno.loadDesc = yes
panTro2.genbank.est.native.load = yes
panTro2.upstreamGeneTbl = refGene

# Gorilla - refseq assembly: GCF_008122165.1
gorGor6.serverGenome = /hive/data/genomes/gorGor6/gorGor6.2bit
gorGor6.ooc = /hive/data/genomes/gorGor6/jkStuff/gorGor6.11.ooc
gorGor6.lift = /hive/data/genomes/gorGor6/jkStuff/gorGor6.nonBridged.lft
gorGor6.perChromTables = no
gorGor6.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
gorGor6.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
gorGor6.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
gorGor6.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
gorGor6.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
gorGor6.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
gorGor6.downloadDir = gorGor6
# default yes refseq.mrna.native refseq.mrna.xeno genbank.mrna.native
# default yes genbank.est.native
# default no genbank.mrna.xeno genbank.est.xeno

# Gorilla
gorGor5.serverGenome = /hive/data/genomes/gorGor5/gorGor5.2bit
gorGor5.ooc = /hive/data/genomes/gorGor5/jkStuff/gorGor5.11.ooc
gorGor5.lift = no
gorGor5.perChromTables = no
gorGor5.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
gorGor5.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
gorGor5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
gorGor5.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
gorGor5.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
gorGor5.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
gorGor5.downloadDir = gorGor5
# default yes refseq.mrna.native refseq.mrna.xeno genbank.mrna.native
# default yes genbank.est.native
# default no genbank.mrna.xeno genbank.est.xeno

# Gorilla
gorGor4.serverGenome = /hive/data/genomes/gorGor4/gorGor4.2bit
gorGor4.ooc = /hive/data/genomes/gorGor4/jkStuff/gorGor4.11.ooc
gorGor4.lift = /hive/data/genomes/gorGor4/jkStuff/gorGor4.nonBridged.lft
gorGor4.perChromTables = no
gorGor4.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
gorGor4.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
gorGor4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
gorGor4.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
gorGor4.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
gorGor4.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
gorGor4.downloadDir = gorGor4
# refseq.mrna native and xeno are default yes
# genbank.mrna and genbank.est native are default yes, the xeno is default no
# reset upstream* if and when a multiple alignment is constructed
# gorGor4.upstreamGeneTbl = ensGene
# gorGor4.upstreamMaf = multiz11way /hive/data/genomes/gorGor4/bed/multiz11way/species.list

# Gorilla
gorGor3.serverGenome = /hive/data/genomes/gorGor3/gorGor3.2bit
gorGor3.ooc = /hive/data/genomes/gorGor3/gorGor3.11.ooc
gorGor3.lift = no
gorGor3.perChromTables = no
gorGor3.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
gorGor3.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
gorGor3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
gorGor3.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
gorGor3.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
gorGor3.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
gorGor3.downloadDir = gorGor3
gorGor3.refseq.mrna.native.load  = no
gorGor3.refseq.mrna.xeno.load = yes
gorGor3.refseq.mrna.xeno.loadDesc  = yes
gorGor3.genbank.mrna.xeno.load  = yes
gorGor3.genbank.est.native.load = no
gorGor3.upstreamGeneTbl = ensGene
gorGor3.upstreamMaf = multiz11way /hive/data/genomes/gorGor3/bed/multiz11way/species.list

# Baboon
# papAnu4 (Papio anubis - olive baboon taxId: 9555)
papAnu4.serverGenome = /hive/data/genomes/papAnu4/papAnu4.2bit
papAnu4.ooc = /hive/data/genomes/papAnu4/jkStuff/papAnu4.11.ooc
papAnu4.lift = /hive/data/genomes/papAnu4/jkStuff/nonBridged.lft
papAnu4.perChromTables = no
papAnu4.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
papAnu4.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
papAnu4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
papAnu4.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
papAnu4.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
papAnu4.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
papAnu4.downloadDir = papAnu4
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc

# papAnu3 (baboon)
papAnu3.serverGenome = /hive/data/genomes/papAnu3/papAnu3.2bit
papAnu3.ooc = /hive/data/genomes/papAnu3/jkStuff/papAnu3.11.ooc
papAnu3.lift = /hive/data/genomes/papAnu3/jkStuff/papAnu3.nonBridged.lft
papAnu3.perChromTables = no
papAnu3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
papAnu3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
papAnu3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
papAnu3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
papAnu3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
papAnu3.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
papAnu3.downloadDir = papAnu3
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc

# Baboon
# papAnu2 (baboon)
papAnu2.serverGenome = /hive/data/genomes/papAnu2/papAnu2.2bit
papAnu2.ooc = /hive/data/genomes/papAnu2/jkStuff/papAnu2.11.ooc
papAnu2.lift = /hive/data/genomes/papAnu2/jkStuff/papAnu2.nonBridged.lift
papAnu2.perChromTables = no
papAnu2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
papAnu2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
papAnu2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
papAnu2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
papAnu2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
papAnu2.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
papAnu2.downloadDir = papAnu2
papAnu2.refseq.mrna.native.load  = yes
papAnu2.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
papAnu2.genbank.mrna.xeno.load = yes
papAnu2.genbank.mrna.xeno.loadDesc = yes
papAnu2.genbank.est.native.load = yes

papHam1.serverGenome = /hive/data/genomes/papHam1/papHam1.2bit
papHam1.ooc = /hive/data/genomes/papHam1/papHam1.11.ooc
papHam1.lift = no
papHam1.perChromTables = no
papHam1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
papHam1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
papHam1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
papHam1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
papHam1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
papHam1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
papHam1.downloadDir = papHam1
papHam1.refseq.mrna.native.load  = yes
papHam1.refseq.mrna.xeno.load = yes
papHam1.refseq.mrna.xeno.loadDesc  = yes
papHam1.genbank.est.native.load = no
papHam1.upstreamGeneTbl = xenoRefGene


# ponAbe3 (Orangutan - Pongo abelli - refseq GCF_002880775.1 - taxId 9601)
ponAbe3.serverGenome = /hive/data/genomes/ponAbe3/ponAbe3.2bit
ponAbe3.ooc = /hive/data/genomes/ponAbe3/jkStuff/ponAbe3.11.ooc
ponAbe3.lift = /hive/data/genomes/ponAbe3/jkStuff/ponAbe3.nonBridged.lft
ponAbe3.perChromTables = no
ponAbe3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
ponAbe3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
ponAbe3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
ponAbe3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
ponAbe3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
ponAbe3.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
ponAbe3.downloadDir = ponAbe3
# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
# yes: genbank.est.native.load refseq.mrna.native.load
# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
# yes: refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
# no: genbank.est.native.loadDesc genbank.est.xeno.load
# no: genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse

# Orangutan
ponAbe2.serverGenome = /hive/data/genomes/ponAbe2/ponAbe2.2bit
ponAbe2.ooc = /hive/data/genomes/ponAbe2/11.ooc
ponAbe2.align.unplacedChroms = chrUn,chr*_random
ponAbe2.lift = /hive/data/genomes/ponAbe2/jkStuff/genbank.lft
ponAbe2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
ponAbe2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
ponAbe2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
ponAbe2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
ponAbe2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
ponAbe2.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
ponAbe2.downloadDir = ponAbe2
ponAbe2.refseq.mrna.native.load  = yes
ponAbe2.refseq.mrna.xeno.load = yes
ponAbe2.refseq.mrna.xeno.loadDesc  = yes
ponAbe2.genbank.mrna.xeno.load  = yes
ponAbe2.upstreamGeneTbl = xenoRefGene
ponAbe2.upstreamMaf = multiz8way /hive/data/genomes/ponAbe2/bed/multiz8way/species.list

# nomLeu3 (Gibbon)
nomLeu3.serverGenome = /hive/data/genomes/nomLeu3/nomLeu3.2bit
nomLeu3.ooc = /hive/data/genomes/nomLeu3/nomLeu3.11.ooc
nomLeu3.lift = /hive/data/genomes/nomLeu3/jkStuff/nomLeu3.nonBridged.lift
nomLeu3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
nomLeu3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
nomLeu3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
nomLeu3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
nomLeu3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
nomLeu3.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
nomLeu3.refseq.mrna.native.load  = no
nomLeu3.refseq.mrna.xeno.load = yes
nomLeu3.genbank.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
nomLeu3.genbank.mrna.xeno.load = yes
nomLeu3.genbank.est.native.load = no
nomLeu3.downloadDir = nomLeu3
nomLeu3.perChromTables = no

# nomLeu2 (Gibbon)
nomLeu2.serverGenome = /hive/data/genomes/nomLeu2/nomLeu2.2bit
nomLeu2.ooc = /hive/data/genomes/nomLeu2/nomLeu2.11.ooc
nomLeu2.lift = no
nomLeu2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
nomLeu2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
nomLeu2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
nomLeu2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
nomLeu2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
nomLeu2.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
nomLeu2.refseq.mrna.native.load  = no
nomLeu2.refseq.mrna.xeno.load = yes
nomLeu2.genbank.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
nomLeu2.genbank.est.native.load = no
nomLeu2.downloadDir = nomLeu2
nomLeu2.perChromTables = no

# nomLeu1 (Gibbon)
nomLeu1.serverGenome = /hive/data/genomes/nomLeu1/nomLeu1.2bit
nomLeu1.ooc = /hive/data/genomes/nomLeu1/nomLeu1.11.ooc
nomLeu1.lift = no
nomLeu1.perChromTables = no
nomLeu1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
nomLeu1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
nomLeu1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
nomLeu1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
nomLeu1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
nomLeu1.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
nomLeu1.downloadDir = nomLeu1
nomLeu1.refseq.mrna.native.load  = no
nomLeu1.refseq.mrna.xeno.load = yes
nomLeu1.refseq.mrna.xeno.loadDesc  = yes
nomLeu1.genbank.mrna.native.load = yes
nomLeu1.genbank.mrna.native.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
nomLeu1.genbank.est.native.load = no
nomLeu1.genbank.est.native.loadDesc = no

# macNem1 (pig-tailed macaque)
macNem1.serverGenome = /hive/data/genomes/macNem1/macNem1.2bit
macNem1.ooc = /hive/data/genomes/macNem1/jkStuff/macNem1.11.ooc
macNem1.lift = no
macNem1.perChromTables = no
macNem1.downloadDir = macNem1
macNem1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
macNem1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
macNem1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
macNem1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
macNem1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults are fine: genbank.mrna.native refseq.mrna.native refseq.mrna.xeno yes
# and genbank.est.native
# macNem1.upstreamGeneTbl = refGene
# macNem1.upstreamMaf = multiz7way
# /hive/data/genomes/macNem1/bed/multiz7way/species.lst

# macFas5 (Crab-eating macaque)
macFas5.serverGenome = /hive/data/genomes/macFas5/macFas5.2bit
macFas5.ooc = /hive/data/genomes/macFas5/jkStuff/macFas5.11.ooc
macFas5.lift = /hive/data/genomes/macFas5/jkStuff/macFas5.nonBridged.lft
macFas5.perChromTables = no
macFas5.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
macFas5.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
macFas5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
macFas5.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
macFas5.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
macFas5.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
macFas5.downloadDir = macFas5
macFas5.refseq.mrna.native.load  = yes
macFas5.refseq.mrna.native.loadDesc  = yes
macFas5.refseq.mrna.xeno.load = yes
macFas5.refseq.mrna.xeno.loadDesc  = yes
macFas5.genbank.mrna.native.load  = yes
macFas5.genbank.mrna.native.loadDesc  = yes
macFas5.genbank.est.native.load  = yes
macFas5.upstreamGeneTbl = refGene

# rheMac10 Macaca mulatta (rhesus) (refseq assembly GCF_003339765.1)
rheMac10.serverGenome = /hive/data/genomes/rheMac10/rheMac10.2bit
rheMac10.ooc = /hive/data/genomes/rheMac10/jkStuff/rheMac10.11.ooc
rheMac10.lift = /hive/data/genomes/rheMac10/jkStuff/rheMac10.nonBridged.lft
rheMac10.perChromTables = no
rheMac10.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
rheMac10.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
rheMac10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
rheMac10.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
rheMac10.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
rheMac10.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
rheMac10.downloadDir = rheMac10
# DO NOT NEED genbank.mrna.xeno except for human, mouse(and in this case rhesus)
rheMac10.refseq.mrna.native.load  = yes
rheMac10.refseq.mrna.xeno.load  = yes
rheMac10.upstreamGeneTbl = refGene

# rheMac8 Macaca mulatta (rhesus)
rheMac8.serverGenome = /hive/data/genomes/rheMac8/rheMac8.2bit
rheMac8.ooc = /hive/data/genomes/rheMac8/jkStuff/rheMac8.11.ooc
rheMac8.lift = /hive/data/genomes/rheMac8/jkStuff/nonBridged.lft
rheMac8.perChromTables = no
rheMac8.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
rheMac8.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
rheMac8.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
rheMac8.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
rheMac8.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
rheMac8.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
rheMac8.downloadDir = rheMac8
# DO NOT NEED genbank.mrna.xeno except for human, mouse(and in this case rhesus)
rheMac8.refseq.mrna.native.load  = yes
rheMac8.refseq.mrna.xeno.load  = yes
rheMac8.upstreamGeneTbl = refGene

# Rhesus macaque (macaca mulatta)
rheMac2.serverGenome = /hive/data/genomes/rheMac2/rheMac2.2bit
rheMac2.ooc = /hive/data/genomes/rheMac2/11.ooc
rheMac2.lift = no
rheMac2.downloadDir = rheMac2
rheMac2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
rheMac2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
rheMac2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
rheMac2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
rheMac2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
rheMac2.genbank.mrna.xeno.load = yes
rheMac2.refseq.mrna.native.load  = yes
rheMac2.refseq.mrna.xeno.load  = yes
rheMac2.perChromTables = no
rheMac2.upstreamGeneTbl = refGene

# rheMac3 Rhesus macaque (macaca mulatta)
rheMac3.serverGenome = /hive/data/genomes/rheMac3/rheMac3.2bit
rheMac3.ooc = /hive/data/genomes/rheMac3/rheMac3.11.ooc
rheMac3.lift = no
rheMac3.perChromTables = no
rheMac3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
rheMac3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
rheMac3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
rheMac3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
rheMac3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
rheMac3.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
rheMac3.downloadDir = rheMac3
# DO NOT NEED genbank.mrna.xeno except for human, mouse
rheMac3.genbank.mrna.xeno.load = yes
rheMac3.refseq.mrna.native.load  = yes
rheMac3.refseq.mrna.xeno.load  = yes
rheMac3.upstreamGeneTbl = refGene

# chlSab2 (green monkey) (2,004 scaffolds N50 101219884)
chlSab2.serverGenome = /hive/data/genomes/chlSab2/chlSab2.2bit
chlSab2.ooc = /hive/data/genomes/chlSab2/jkStuff/chlSab2.11.ooc
chlSab2.lift = /hive/data/genomes/chlSab2/jkStuff/chlSab2.nonBridged.lft
chlSab2.perChromTables = no
chlSab2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
chlSab2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
chlSab2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
chlSab2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
chlSab2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
chlSab2.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
chlSab2.downloadDir = chlSab2
chlSab2.refseq.mrna.native.load  = no
chlSab2.refseq.mrna.xeno.load = yes
chlSab2.refseq.mrna.xeno.loadDesc  = yes
chlSab2.genbank.mrna.native.load = yes
chlSab2.genbank.mrna.native.loadDesc = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
chlSab2.genbank.mrna.xeno.load = no
chlSab2.genbank.mrna.xeno.loadDesc = no
chlSab2.genbank.est.native.load = yes
chlSab2.genbank.est.native.loadDesc = yes
# chlSab2.upstreamGeneTbl = ensGene

# colAng1 (Colobus angolensis palliatus) (13,124 contigs, 86.6X coverage)
colAng1.serverGenome = /hive/data/genomes/colAng1/colAng1.2bit
colAng1.ooc = /hive/data/genomes/colAng1/jkStuff/colAng1.11.ooc
colAng1.lift = no
colAng1.perChromTables = no
colAng1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
colAng1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
colAng1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
colAng1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
colAng1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
colAng1.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
colAng1.downloadDir = colAng1
# default yes refseq.mrna.native refseq.mrna.xeno genbank.mrna.native
# default yes genbank.est.native
# default no genbank.mrna.xeno genbank.est.xeno
# colAng1.upstreamGeneTbl = ncbiGene

# rhiBie1 - Rhinopithecus bieti - black snub-nosed monkey taxId 61621
rhiBie1.serverGenome = /hive/data/genomes/rhiBie1/rhiBie1.2bit
rhiBie1.ooc = /hive/data/genomes/rhiBie1/jkStuff/rhiBie1.11.ooc
rhiBie1.lift = no
rhiBie1.perChromTables = no
rhiBie1.downloadDir = rhiBie1
rhiBie1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
rhiBie1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
rhiBie1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
rhiBie1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
rhiBie1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults are fine: genbank.mrna.native refseq.mrna.native refseq.mrna.xeno yes
# and genbank.est.native
# rhiBie1.upstreamGeneTbl = refGene
# rhiBie1.upstreamMaf = multiz7way
# /hive/data/genomes/melGal4/bed/multiz7way/species.lst

# rhiRox1 (Golden snub-nosed monkey)
rhiRox1.serverGenome = /hive/data/genomes/rhiRox1/rhiRox1.2bit
rhiRox1.ooc = /hive/data/genomes/rhiRox1/jkStuff/rhiRox1.11.ooc
rhiRox1.lift = no
rhiRox1.perChromTables = no
rhiRox1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
rhiRox1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
rhiRox1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
rhiRox1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
rhiRox1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
rhiRox1.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
rhiRox1.downloadDir = rhiRox1
rhiRox1.refseq.mrna.native.load  = no
rhiRox1.refseq.mrna.native.loadDesc  = no
rhiRox1.refseq.mrna.xeno.load = yes
rhiRox1.refseq.mrna.xeno.loadDesc  = yes
rhiRox1.genbank.mrna.native.load  = no
rhiRox1.genbank.mrna.native.loadDesc  = no
rhiRox1.genbank.est.native.load  = no
# rhiRox1.upstreamGeneTbl = refGene

# nasLar1 (Proboscis monkey)
nasLar1.serverGenome = /hive/data/genomes/nasLar1/nasLar1.2bit
nasLar1.ooc = /hive/data/genomes/nasLar1/jkStuff/nasLar1.11.ooc
nasLar1.lift = /hive/data/genomes/nasLar1/jkStuff/nasLar1.nonBridged.lft
nasLar1.perChromTables = no
nasLar1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
nasLar1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
nasLar1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
nasLar1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
nasLar1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
nasLar1.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
nasLar1.downloadDir = nasLar1
nasLar1.refseq.mrna.native.load  = no
nasLar1.refseq.mrna.native.loadDesc  = no
nasLar1.refseq.mrna.xeno.load = yes
nasLar1.refseq.mrna.xeno.loadDesc  = yes
nasLar1.genbank.mrna.native.load  = no
nasLar1.genbank.mrna.native.loadDesc  = no
nasLar1.genbank.est.native.load  = no
nasLar1.upstreamGeneTbl = xenoRefGene

# turTru2 (Dolphin)
turTru2.serverGenome = /hive/data/genomes/turTru2/turTru2.2bit
turTru2.ooc = /hive/data/genomes/turTru2/turTru2.11.ooc
turTru2.lift = no
turTru2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
turTru2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
turTru2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
turTru2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
turTru2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
turTru2.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
turTru2.refseq.mrna.native.load  = no
turTru2.refseq.mrna.xeno.load = yes
turTru2.genbank.mrna.native.load = no
turTru2.genbank.mrna.xeno.load = no
turTru2.genbank.est.native.load = no
turTru2.downloadDir = turTru2
turTru2.perChromTables = no

# galGal2 (chicken)
galGal2.serverGenome = /hive/data/genomes/galGal2/galGal2.2bit
galGal2.ooc = /hive/data/genomes/galGal2/11.ooc
galGal2.lift = /hive/data/genomes/galGal2/jkStuff/liftAll.lft
galGal2.align.unplacedChroms = chrUn
galGal2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
galGal2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
galGal2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
galGal2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
galGal2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
galGal2.refseq.mrna.native.load = yes
galGal2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
galGal2.genbank.mrna.xeno.load = yes
galGal2.downloadDir = galGal2
galGal2.upstreamGeneTbl = refGene
galGal2.upstreamMaf = multiz7way /hive/data/genomes/galGal2/bed/multiz7way/species.lst

# galGal3
galGal3.serverGenome = /hive/data/genomes/galGal3/galGal3.2bit
galGal3.ooc = /hive/data/genomes/galGal3/11.ooc
galGal3.align.unplacedChroms = chr*_random
galGal3.lift = /hive/data/genomes/galGal3/jkStuff/liftAll.lft
galGal3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
galGal3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
galGal3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
galGal3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
galGal3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
galGal3.refseq.mrna.native.load = yes
galGal3.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
galGal3.genbank.mrna.xeno.load = yes
galGal3.downloadDir = galGal3
galGal3.upstreamGeneTbl = refGene
galGal3.upstreamMaf = multiz7way /hive/data/genomes/galGal3/bed/multiz7way/species.lst

# galGal6 (chicken/GCF_000002315.5_GRCg6a)
galGal6.serverGenome = /hive/data/genomes/galGal6/galGal6.2bit
galGal6.ooc = /hive/data/genomes/galGal6/jkStuff/galGal6.11.ooc
galGal6.lift = /hive/data/genomes/galGal6/jkStuff/nonBridged.lft
galGal6.perChromTables = no
galGal6.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
galGal6.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
galGal6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
galGal6.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
galGal6.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
galGal6.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
galGal6.refseq.mrna.native.load = yes
galGal6.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
galGal6.genbank.mrna.xeno.load = yes
galGal6.downloadDir = galGal6
# galGal6.upstreamGeneTbl = refGene
# galGal6.upstreamMaf = multiz7way /hive/data/genomes/galGal4/bed/multiz7way/species.lst


# galGal5 (chicken)
galGal5.serverGenome = /hive/data/genomes/galGal5/galGal5.2bit
galGal5.ooc = /hive/data/genomes/galGal5/jkStuff/galGal5.11.ooc
galGal5.lift = /hive/data/genomes/galGal5/jkStuff/nonBridged.lft
galGal5.perChromTables = no
galGal5.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
galGal5.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
galGal5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
galGal5.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
galGal5.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
galGal5.refseq.mrna.native.load = yes
galGal5.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
galGal5.genbank.mrna.xeno.load = yes
galGal5.downloadDir = galGal5
# galGal5.upstreamGeneTbl = refGene
# galGal5.upstreamMaf = multiz7way /hive/data/genomes/galGal4/bed/multiz7way/species.lst

# galGal4 (chicken)
galGal4.serverGenome = /hive/data/genomes/galGal4/galGal4.2bit
galGal4.ooc = /hive/data/genomes/galGal4/jkStuff/galGal4.11.ooc
galGal4.lift = /hive/data/genomes/galGal4/jkStuff/galGal4.nonBridged.lift
galGal4.perChromTables = no
galGal4.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
galGal4.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
galGal4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
galGal4.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
galGal4.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
galGal4.refseq.mrna.native.load = yes
galGal4.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
galGal4.genbank.mrna.xeno.load = yes
galGal4.downloadDir = galGal4
# galGal4.upstreamGeneTbl = refGene
# galGal4.upstreamMaf = multiz7way /hive/data/genomes/galGal3/bed/multiz7way/species.lst

# cotJap2 (Japanese quail/GCF_001577835.1_Coturnix_japonica_2.0)
cotJap2.serverGenome = /hive/data/genomes/cotJap2/cotJap2.2bit
cotJap2.ooc = /hive/data/genomes/cotJap2/jkStuff/cotJap2.11.ooc
cotJap2.lift = /hive/data/genomes/cotJap2/jkStuff/nonBridged.lft
cotJap2.perChromTables = no
cotJap2.downloadDir = cotJap2
cotJap2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
cotJap2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
cotJap2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
cotJap2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
cotJap2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
cotJap2.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# cotJap2.upstreamGeneTbl = refGene
# cotJap2.upstreamMaf = multiz7way /hive/data/genomes/galGal4/bed/multiz7way/species.lst

# melGal5 (turkey)
melGal5.serverGenome = /hive/data/genomes/melGal5/melGal5.2bit
melGal5.ooc = /hive/data/genomes/melGal5/jkStuff/melGal5.11.ooc
melGal5.lift = /hive/data/genomes/melGal5/jkStuff/nonBridged.lft
melGal5.perChromTables = no
melGal5.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
melGal5.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
melGal5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
melGal5.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
melGal5.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
melGal5.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
melGal5.downloadDir = melGal5
melGal5.refseq.mrna.native.load  = yes
melGal5.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# melGal5.upstreamGeneTbl = ensGene

# melGal1 (turkey)
melGal1.serverGenome = /hive/data/genomes/melGal1/melGal1.2bit
melGal1.ooc = /hive/data/genomes/melGal1/melGal1.11.ooc
melGal1.lift = no
melGal1.perChromTables = no
melGal1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
melGal1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
melGal1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
melGal1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
melGal1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
melGal1.downloadDir = melGal1
melGal1.refseq.mrna.native.load  = no
melGal1.refseq.mrna.xeno.load = yes
melGal1.refseq.mrna.xeno.loadDesc  = yes
melGal1.genbank.mrna.native.load = yes
melGal1.genbank.mrna.native.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
melGal1.genbank.mrna.xeno.load = yes
melGal1.genbank.mrna.xeno.loadDesc = yes
melGal1.genbank.est.native.load = yes
melGal1.genbank.est.native.loadDesc = yes
melGal1.upstreamGeneTbl = ensGene

# aquChr2 (golden eagle)
aquChr2.serverGenome = /hive/data/genomes/aquChr2/aquChr2.2bit
aquChr2.ooc = /hive/data/genomes/aquChr2/jkStuff/aquChr2.11.ooc
aquChr2.lift = no
aquChr2.perChromTables = no
aquChr2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
aquChr2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
aquChr2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
aquChr2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
aquChr2.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
aquChr2.downloadDir = aquChr2
aquChr2.refseq.mrna.native.load  = no
aquChr2.refseq.mrna.xeno.load = yes
aquChr2.refseq.mrna.xeno.loadDesc  = yes
aquChr2.genbank.mrna.native.load = no
aquChr2.genbank.mrna.native.loadDesc = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
aquChr2.genbank.est.native.load = no
aquChr2.genbank.est.native.loadDesc = no
# aquChr2.upstreamGeneTbl = ensGene

# myoLuc2 (Microbat)
myoLuc2.serverGenome = /hive/data/genomes/myoLuc2/myoLuc2.2bit
myoLuc2.ooc = /hive/data/genomes/myoLuc2/myoLuc2.11.ooc
myoLuc2.lift = no
myoLuc2.perChromTables = no
myoLuc2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
myoLuc2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
myoLuc2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
myoLuc2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
myoLuc2.downloadDir = myoLuc2
myoLuc2.refseq.mrna.native.load  = no
myoLuc2.refseq.mrna.xeno.load = yes
myoLuc2.refseq.mrna.xeno.loadDesc = yes
myoLuc2.genbank.mrna.native.load = yes
myoLuc2.genbank.mrna.native.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
myoLuc2.genbank.mrna.xeno.load = yes
myoLuc2.genbank.mrna.xeno.loadDesc = yes
myoLuc2.genbank.est.native.load = no
myoLuc2.genbank.est.native.loadDesc = no
myoLuc2.upstreamGeneTbl = ensGene

# allMis1 - Alligator mississippiensis
allMis1.serverGenome = /hive/data/genomes/allMis1/allMis1.2bit
allMis1.ooc = /hive/data/genomes/allMis1/jkStuff/allMis1.11.ooc
allMis1.lift = no
allMis1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
allMis1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
allMis1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
allMis1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
allMis1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
allMis1.refseq.mrna.native.load = yes
allMis1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
allMis1.genbank.mrna.xeno.load = yes
allMis1.downloadDir = allMis1
allMis1.perChromTables = no

# taeGut2 - Zebra Finch
taeGut2.serverGenome = /hive/data/genomes/taeGut2/taeGut2.2bit
taeGut2.ooc = /hive/data/genomes/taeGut2/jkStuff/taeGut2.11.ooc
taeGut2.align.unplacedChroms = chrUn_*,chr*_random
taeGut2.lift = /hive/data/genomes/taeGut2/jkStuff/taeGut2.nonBridged.lift
taeGut2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
taeGut2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
taeGut2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
taeGut2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
taeGut2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
taeGut2.refseq.mrna.native.load = yes
taeGut2.refseq.mrna.xeno.load = yes
taeGut2.downloadDir = taeGut2
taeGut2.upstreamGeneTbl = refGene
taeGut2.perChromTables = no

# taeGut1
taeGut1.serverGenome = /hive/data/genomes/taeGut1/taeGut1.2bit
taeGut1.ooc = /hive/data/genomes/taeGut1/taeGut1.11.ooc
taeGut1.align.unplacedChroms = chrUn,chr*_random
taeGut1.lift = /hive/data/genomes/taeGut1/jkStuff/liftAll.lft
taeGut1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
taeGut1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
taeGut1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
taeGut1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
taeGut1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
taeGut1.refseq.mrna.native.load = yes
taeGut1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
taeGut1.genbank.mrna.xeno.load = yes
taeGut1.downloadDir = taeGut1
taeGut1.upstreamGeneTbl = refGene

# ce11 (C. elegans)
ce11.serverGenome = /hive/data/genomes/ce11/ce11.2bit
ce11.ooc = /hive/data/genomes/ce11/jkStuff/ce11.11.ooc
ce11.perChromTables = no
ce11.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
ce11.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
ce11.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
ce11.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
ce11.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
ce11.maxIntron = 100000
ce11.lift = no
ce11.refseq.mrna.native.load = yes
ce11.refseq.mrna.xeno.load = yes
ce11.genbank.mrna.xeno.load = yes
ce11.genbank.mrna.native.load = yes
ce11.genbank.est.native.load = yes
ce11.downloadDir = ce11
# ce11.upstreamGeneTbl = ensGene
# ce11.upstreamMaf = multiz7way /hive/data/genomes/ce11/bed/multiz7way/species.list

# ce10 (C. elegans)
ce10.serverGenome = /hive/data/genomes/ce10/ce10.2bit
ce10.ooc = /hive/data/genomes/ce10/ce10.11.ooc
ce10.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
ce10.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
ce10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
ce10.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
ce10.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
ce10.maxIntron = 100000
ce10.lift = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
ce10.genbank.mrna.xeno.load = yes
ce10.refseq.mrna.xeno.load = yes
ce10.downloadDir = ce10
ce10.upstreamGeneTbl = ensGene
ce10.upstreamMaf = multiz7way /hive/data/genomes/ce10/bed/multiz7way/species.list

# ce6 (C. elegans)
ce6.serverGenome = /hive/data/genomes/ce6/ce6.2bit
ce6.ooc = /hive/data/genomes/ce6/11.ooc
ce6.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
ce6.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
ce6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
ce6.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
ce6.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
ce6.maxIntron = 100000
ce6.lift = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
ce6.genbank.mrna.xeno.load = yes
ce6.refseq.mrna.xeno.load = yes
ce6.downloadDir = ce6
ce6.upstreamGeneTbl = ensGene
ce6.upstreamMaf = multiz6way /hive/data/genomes/ce6/bed/multiz6way/species.lst

# ce4 (C. elegans)
ce4.serverGenome = /hive/data/genomes/ce4/ce4.2bit
ce4.ooc = /hive/data/genomes/ce4/11.ooc
ce4.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
ce4.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
ce4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
ce4.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
ce4.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
ce4.maxIntron = 100000
ce4.lift = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
ce4.refseq.mrna.xeno.load = yes
ce4.downloadDir = ce4
ce4.upstreamGeneTbl = refGene
ce4.upstreamMaf = multiz5way /hive/data/genomes/ce4/bed/multiz5way/species.lst

# ce2 (C. elegans)
ce2.serverGenome = /hive/data/genomes/ce2/nib/chr*.nib
ce2.ooc = /hive/data/genomes/ce2/11.ooc
ce2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
ce2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
ce2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
ce2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
ce2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
ce2.maxIntron = 100000
ce2.lift = no
ce2.genbank.mrna.xeno.load = no
ce2.downloadDir = ce2
ce2.upstreamGeneTbl = refGene

# choHof1 (sloth)
choHof1.serverGenome = /hive/data/genomes/choHof1/choHof1.2bit
choHof1.ooc = /hive/data/genomes/choHof1//choHof1.11.ooc
choHof1.lift = no
choHof1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
choHof1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
choHof1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
choHof1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
choHof1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
choHof1.refseq.mrna.native.load = no
choHof1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
choHof1.genbank.mrna.xeno.load = yes
choHof1.genbank.est.native.load = no
choHof1.downloadDir = choHof1
choHof1.perChromTables = no

# chrPic2 (green painted turtle)
chrPic2.serverGenome = /hive/data/genomes/chrPic2/chrPic2.2bit
chrPic2.ooc = /hive/data/genomes/chrPic2/jkStuff/chrPic2.11.ooc
chrPic2.lift = /hive/data/genomes/chrPic2/jkStuff/chrPic2.nonBridged.lift
chrPic2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
chrPic2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
chrPic2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
chrPic2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
chrPic2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
chrPic2.refseq.mrna.native.load = no
chrPic2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
chrPic2.genbank.est.native.load = no
chrPic2.downloadDir = chrPic2
chrPic2.perChromTables = no

# chrPic1 (green painted turtle)
chrPic1.serverGenome = /hive/data/genomes/chrPic1/chrPic1.2bit
chrPic1.ooc = /hive/data/genomes/chrPic1/jkStuff/chrPic1.11.ooc
chrPic1.lift = no
chrPic1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
chrPic1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
chrPic1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
chrPic1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
chrPic1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
chrPic1.refseq.mrna.native.load = no
chrPic1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
chrPic1.genbank.mrna.xeno.load = yes
chrPic1.genbank.est.native.load = no
chrPic1.downloadDir = chrPic1
chrPic1.perChromTables = no

# dasNov3 (armadillo)
dasNov3.serverGenome = /hive/data/genomes/dasNov3/dasNov3.2bit
dasNov3.ooc = /hive/data/genomes/dasNov3/jkStuff/dasNov3.11.ooc
dasNov3.lift = no
dasNov3.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
dasNov3.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
dasNov3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
dasNov3.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
dasNov3.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
dasNov3.refseq.mrna.native.load = no
dasNov3.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dasNov3.genbank.mrna.xeno.load = yes
dasNov3.genbank.est.native.load = no
dasNov3.downloadDir = dasNov3
dasNov3.perChromTables = no

# casCan1 (American beaver/Castor canadensis/taxId 51338)
casCan1.serverGenome = /hive/data/genomes/casCan1/casCan1.2bit
casCan1.ooc = /hive/data/genomes/casCan1/jkStuff/casCan1.11.ooc
casCan1.lift = no
casCan1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
casCan1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
casCan1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
casCan1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
casCan1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
casCan1.genbank.est.xeno.pslCDnaFilter  = ${ordered.genbank.est.xeno.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
# yes: genbank.est.native.load refseq.mrna.native.load
# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
# yes: refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
# no: genbank.est.native.loadDesc genbank.est.xeno.load
# no: genbank.est.xeno.loadDesc
# there are zero native est or refSeq for casCan1
casCan1.genbank.est.native.load = no
casCan1.refseq.mrna.native.load = no
casCan1.refseq.mrna.native.loadDesc = no
casCan1.downloadDir = casCan1
casCan1.perChromTables = no

# dipOrd2 (Kangaroo rat)
dipOrd2.serverGenome = /hive/data/genomes/dipOrd2/dipOrd2.2bit
dipOrd2.ooc = /hive/data/genomes/dipOrd2/jkStuff/dipOrd2.11.ooc
dipOrd2.lift = no
dipOrd2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
dipOrd2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
dipOrd2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
dipOrd2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
dipOrd2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# there are zero native mrna or est for dipOrd
dipOrd2.refseq.mrna.native.load = no
dipOrd2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dipOrd2.genbank.mrna.xeno.load = yes
dipOrd2.genbank.est.native.load = no
dipOrd2.downloadDir = dipOrd2
dipOrd2.perChromTables = no

# dipOrd1 (Kangaroo rat)
dipOrd1.serverGenome = /hive/data/genomes/dipOrd1/dipOrd1.2bit
dipOrd1.ooc = /hive/data/genomes/dipOrd1/dipOrd1.11.ooc
dipOrd1.lift = no
dipOrd1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
dipOrd1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
dipOrd1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
dipOrd1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
dipOrd1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
dipOrd1.refseq.mrna.native.load = no
dipOrd1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dipOrd1.genbank.mrna.xeno.load = yes
dipOrd1.genbank.est.native.load = no
dipOrd1.downloadDir = dipOrd1
dipOrd1.perChromTables = no

# eriEur2 (European Hedgehog)
eriEur2.serverGenome = /hive/data/genomes/eriEur2/eriEur2.2bit
eriEur2.ooc = /hive/data/genomes/eriEur2/jkStuff/eriEur2.11.ooc
eriEur2.lift = no
eriEur2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
eriEur2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
eriEur2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
eriEur2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
eriEur2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
eriEur2.refseq.mrna.native.load = no
eriEur2.refseq.mrna.xeno.load = yes
eriEur2.genbank.mrna.xeno.load = no
eriEur2.genbank.est.native.load = no
eriEur2.downloadDir = eriEur2
eriEur2.perChromTables = no

# eriEur1 (European Hedgehog)
eriEur1.serverGenome = /hive/data/genomes/eriEur1/eriEur1.2bit
eriEur1.ooc = /hive/data/genomes/eriEur1/eriEur1.11.ooc
eriEur1.lift = no
eriEur1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
eriEur1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
eriEur1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
eriEur1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
eriEur1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
eriEur1.refseq.mrna.native.load = no
eriEur1.refseq.mrna.xeno.load = yes
eriEur1.genbank.mrna.xeno.load = no
eriEur1.genbank.est.native.load = no
eriEur1.downloadDir = eriEur1
eriEur1.perChromTables = no

# eulFla1 (Sclater's lemur / Eulemur flavifrons / taxId 87288)
eulFla1.serverGenome = /hive/data/genomes/eulFla1/eulFla1.2bit
eulFla1.ooc = /hive/data/genomes/eulFla1/jkStuff/eulFla1.11.ooc
eulFla1.lift = no
eulFla1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
eulFla1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
eulFla1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
eulFla1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
eulFla1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
eulFla1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
eulFla1.downloadDir = eulFla1
# there are no refseq mrna native
eulFla1.refseq.mrna.native.load  = no
eulFla1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
eulFla1.genbank.mrna.xeno.load = no
eulFla1.genbank.mrna.native.load = no
eulFla1.genbank.est.native.load = no
eulFla1.perChromTables = no

# eulMac1 (Black lemur / Eulemur macaco / taxId 30602)
eulMac1.serverGenome = /hive/data/genomes/eulMac1/eulMac1.2bit
eulMac1.ooc = /hive/data/genomes/eulMac1/jkStuff/eulMac1.11.ooc
eulMac1.lift = no
eulMac1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
eulMac1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
eulMac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
eulMac1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
eulMac1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
eulMac1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
eulMac1.downloadDir = eulMac1
# there are no refseq mrna native
eulMac1.refseq.mrna.native.load  = no
eulMac1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
eulMac1.genbank.mrna.xeno.load = no
eulMac1.genbank.mrna.native.load = no
eulMac1.genbank.est.native.load = no
eulMac1.perChromTables = no

# gadMor1 (Atlantic cod)
gadMor1.serverGenome = /hive/data/genomes/gadMor1/gadMor1.2bit
gadMor1.ooc = /hive/data/genomes/gadMor1/jkStuff/gadMor1.11.ooc
gadMor1.lift = no
gadMor1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
gadMor1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
gadMor1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
gadMor1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
gadMor1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
gadMor1.refseq.mrna.native.load = no
gadMor1.refseq.mrna.xeno.load = yes
gadMor1.genbank.mrna.xeno.load = no
gadMor1.genbank.est.native.load = yes
gadMor1.downloadDir = gadMor1
gadMor1.perChromTables = no

# aptMan1 (brown kiwi)
aptMan1.serverGenome = /hive/data/genomes/aptMan1/aptMan1.2bit
aptMan1.ooc = /hive/data/genomes/aptMan1/jkStuff/aptMan1.11.ooc
aptMan1.lift = no
aptMan1.perChromTables = no
aptMan1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
aptMan1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
aptMan1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
aptMan1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
aptMan1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
aptMan1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
aptMan1.downloadDir = aptMan1
# defaults are OK: genbank and refseq mrna.native.load yes
#                  genbank est.native.load yes refseq.mrna.xeno.load yes
#                  genbank mrna and est xeno.load no

# ficAlb1 (Ficedula albicollis - collard flycatcher) - taxId: 59894
ficAlb1.serverGenome = /hive/data/genomes/ficAlb1/ficAlb1.2bit
ficAlb1.ooc = /hive/data/genomes/ficAlb1/jkStuff/ficAlb1.11.ooc
ficAlb1.lift = /hive/data/genomes/ficAlb1/jkStuff/nonBridged.lft
ficAlb1.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
ficAlb1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
ficAlb1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
ficAlb1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
ficAlb1.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# defaults yes: genbank.mrna.native.load and loadDesc
# defaults yes: genbank.est.native.load
# defaults yes: refseq.mrna.native.load, refseq.mrna.native.loadDesc
# defaults yes: refseq.mrna.xeno.load, refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load and loadDesc
# defaults no: genbank.est.xeno.load, genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# there are no genbank.est natives:
ficAlb1.genbank.est.native.load = no
ficAlb1.downloadDir = ficAlb1
ficAlb1.perChromTables = no

# geoFor1 (Medium Ground Finch - Darwin finch)
geoFor1.serverGenome = /hive/data/genomes/geoFor1/geoFor1.2bit
geoFor1.ooc = /hive/data/genomes/geoFor1/jkStuff/geoFor1.11.ooc
geoFor1.lift = no
geoFor1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
geoFor1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
geoFor1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
geoFor1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
geoFor1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
geoFor1.refseq.mrna.native.load = no
geoFor1.refseq.mrna.xeno.load = yes
geoFor1.genbank.mrna.xeno.load = no
geoFor1.genbank.est.native.load = no
geoFor1.downloadDir = geoFor1
geoFor1.perChromTables = no
geoFor1.upstreamGeneTbl = xenoRefGene
geoFor1.upstreamMaf = multiz7way /hive/data/genomes/geoFor1/bed/multiz7way/species.list

# latCha1 (Coelacanth)
latCha1.serverGenome = /hive/data/genomes/latCha1/latCha1.2bit
latCha1.ooc = /hive/data/genomes/latCha1/jkStuff/latCha1.11.ooc
latCha1.lift = no
latCha1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
latCha1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
latCha1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
latCha1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
latCha1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
latCha1.refseq.mrna.native.load = no
latCha1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
latCha1.genbank.mrna.xeno.load = yes
latCha1.genbank.est.native.load = no
latCha1.downloadDir = latCha1
latCha1.perChromTables = no

# manPen1 (Pangolin) 92770 contigs
manPen1.serverGenome = /hive/data/genomes/manPen1/manPen1.2bit
manPen1.ooc = /hive/data/genomes/manPen1/jkStuff/manPen1.11.ooc
manPen1.lift = no
manPen1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
manPen1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
manPen1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
manPen1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
manPen1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
manPen1.refseq.mrna.native.load = no
manPen1.refseq.mrna.xeno.load = yes
manPen1.genbank.mrna.xeno.load = no
manPen1.genbank.mrna.native.load = no
manPen1.genbank.est.native.load = no
manPen1.downloadDir = manPen1
manPen1.perChromTables = no

# melUnd1 (Budgerigar)
melUnd1.serverGenome = /hive/data/genomes/melUnd1/melUnd1.2bit
melUnd1.ooc = /hive/data/genomes/melUnd1/jkStuff/melUnd1.11.ooc
melUnd1.lift = no
melUnd1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
melUnd1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
melUnd1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
melUnd1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
melUnd1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
melUnd1.refseq.mrna.native.load = no
melUnd1.refseq.mrna.xeno.load = yes
melUnd1.genbank.mrna.xeno.load = no
melUnd1.genbank.est.native.load = no
melUnd1.downloadDir = melUnd1
melUnd1.perChromTables = no

# galVar1 - Galeopterus variegatus - Malayan flying lemur
galVar1.serverGenome = /hive/data/genomes/galVar1/galVar1.2bit
galVar1.ooc = /hive/data/genomes/galVar1/jkStuff/galVar1.11.ooc
galVar1.lift = no
galVar1.perChromTables = no
galVar1.downloadDir = galVar1
galVar1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
galVar1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
galVar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
galVar1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
galVar1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
galVar1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# the defaults: genbank.mrna.native.load, yes genbank.est.native.load yes
# refseq.mrna.native.load yes, refseq.mrna.xeno.load yes
# are good enough even though nothing exists for 'native' for this one
# galVar1.upstreamGeneTbl = refGene

# micMur3 (Mouse lemur)
micMur3.serverGenome = /hive/data/genomes/micMur3/micMur3.2bit
micMur3.ooc = /hive/data/genomes/micMur3/jkStuff/micMur3.11.ooc
micMur3.lift = no
micMur3.perChromTables = no
micMur3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
micMur3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
micMur3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
micMur3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
micMur3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
micMur3.refseq.mrna.native.load = no
micMur3.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# the defaults: genbank.mrna.native.load, yes genbank.est.native.load yes
# refseq.mrna.native.load yes, refseq.mrna.xeno.load yes
# there are no native est
micMur3.genbank.est.native.load = no
micMur3.downloadDir = micMur3

# micMur2 (Mouse lemur)
micMur2.serverGenome = /hive/data/genomes/micMur2/micMur2.2bit
micMur2.ooc = /hive/data/genomes/micMur2/jkStuff/micMur2.11.ooc
micMur2.lift = no
micMur2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
micMur2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
micMur2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
micMur2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
micMur2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
micMur2.refseq.mrna.native.load = no
micMur2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
micMur2.genbank.mrna.xeno.load = no
micMur2.genbank.est.native.load = no
micMur2.downloadDir = micMur2
micMur2.perChromTables = no

# micMur1 (Mouse lemur)
micMur1.serverGenome = /hive/data/genomes/micMur1/micMur1.2bit
micMur1.ooc = /hive/data/genomes/micMur1/jkStuff/micMur1.11.ooc
micMur1.lift = no
micMur1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
micMur1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
micMur1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
micMur1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
micMur1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
micMur1.refseq.mrna.native.load = no
micMur1.refseq.mrna.xeno.load = yes
micMur1.genbank.mrna.xeno.load = no
micMur1.genbank.est.native.load = no
micMur1.downloadDir = micMur1
micMur1.perChromTables = no

# ochPri3 (Pika)
ochPri3.serverGenome = /hive/data/genomes/ochPri3/ochPri3.2bit
ochPri3.ooc = /hive/data/genomes/ochPri3/jkStuff/ochPri3.11.ooc
ochPri3.lift = no
ochPri3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
ochPri3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
ochPri3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
ochPri3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
ochPri3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
ochPri3.refseq.mrna.native.load = no
ochPri3.refseq.mrna.xeno.load = yes
ochPri3.genbank.mrna.xeno.load = no
ochPri3.genbank.est.native.load = no
ochPri3.downloadDir = ochPri3
ochPri3.perChromTables = no

# ochPri2 (Pika)
ochPri2.serverGenome = /hive/data/genomes/ochPri2/ochPri2.2bit
ochPri2.ooc = /hive/data/genomes/ochPri2/jkStuff/ochPri2.11.ooc
ochPri2.lift = no
ochPri2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ochPri2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ochPri2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ochPri2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ochPri2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
ochPri2.refseq.mrna.native.load = no
ochPri2.refseq.mrna.xeno.load = yes
ochPri2.genbank.mrna.xeno.load = no
ochPri2.genbank.est.native.load = no
ochPri2.downloadDir = ochPri2
ochPri2.perChromTables = no

# oreNil3 (Nile tilapia)
oreNil3.serverGenome = /hive/data/genomes/oreNil3/oreNil3.2bit
oreNil3.ooc = /hive/data/genomes/oreNil3/jkStuff/oreNil3.11.ooc
oreNil3.lift = no
oreNil3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
oreNil3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
oreNil3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
oreNil3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
oreNil3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
oreNil3.refseq.mrna.native.load = yes
oreNil3.refseq.mrna.xeno.load = yes
oreNil3.genbank.mrna.xeno.load = no
oreNil3.genbank.est.native.load = yes
oreNil3.downloadDir = oreNil3
oreNil3.perChromTables = no

# oreNil2 (Nile tilapia)
oreNil2.serverGenome = /hive/data/genomes/oreNil2/oreNil2.2bit
oreNil2.ooc = /hive/data/genomes/oreNil2/jkStuff/oreNil2.11.ooc
oreNil2.lift = /hive/data/genomes/oreNil2/jkStuff/oreNil2.nonBridged.lift
oreNil2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
oreNil2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
oreNil2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
oreNil2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
oreNil2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
oreNil2.refseq.mrna.native.load = yes
oreNil2.refseq.mrna.xeno.load = yes
oreNil2.genbank.mrna.xeno.load = no
oreNil2.genbank.est.native.load = yes
oreNil2.downloadDir = oreNil2
oreNil2.perChromTables = no

# ascSuu1 (Pig roundworm/Ascaris suum)
ascSuu1.serverGenome = /hive/data/genomes/ascSuu1/ascSuu1.2bit
ascSuu1.ooc = /hive/data/genomes/ascSuu1/jkStuff/ascSuu1.11.ooc
ascSuu1.lift = no
# the nematodes have small introns
ascSuu1.maxIntron = 100000
ascSuu1.perChromTables = no
ascSuu1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ascSuu1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ascSuu1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ascSuu1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ascSuu1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
# refseq.mrna native and xeno are default yes
# genbank.mrna and genbank.est native are default yes, the xeno is default no
ascSuu1.downloadDir = ascSuu1

# priExs1 (P. exspectatus/Pristionchus exspectatus)
priExs1.serverGenome = /hive/data/genomes/priExs1/priExs1.2bit
priExs1.ooc = /hive/data/genomes/priExs1/jkStuff/priExs1.11.ooc
priExs1.lift = /hive/data/genomes/priExs1/jkStuff/priExs1.nonBridged.lft
# the nematodes have small introns
priExs1.maxIntron = 100000
priExs1.perChromTables = no
priExs1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
priExs1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
priExs1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
priExs1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
priExs1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
# refseq.mrna native and xeno are default yes
# genbank.mrna and genbank.est native are default yes, the xeno is default no
priExs1.downloadDir = priExs1

# ancCey1 (A. ceylanicum)
ancCey1.serverGenome = /hive/data/genomes/ancCey1/ancCey1.2bit
ancCey1.ooc = /hive/data/genomes/ancCey1/jkStuff/ancCey1.11.ooc
ancCey1.lift = no
# the nematodes have small introns
ancCey1.maxIntron = 10
ancCey1.perChromTables = no
ancCey1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ancCey1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ancCey1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ancCey1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ancCey1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
# refseq.mrna native and xeno are default yes
# genbank.mrna and genbank.est native are default yes, the xeno is default no
ancCey1.downloadDir = ancCey1

# priPac3 (P. pacificus)
priPac3.serverGenome = /hive/data/genomes/priPac3/priPac3.2bit
priPac3.ooc = /hive/data/genomes/priPac3/jkStuff/priPac3.11.ooc
priPac3.lift = /hive/data/genomes/priPac3/jkStuff/priPac3.nonBridged.lft
priPac3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
priPac3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
priPac3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
priPac3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
priPac3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
priPac3.refseq.mrna.native.load = yes
priPac3.refseq.mrna.xeno.load  = yes
priPac3.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
priPac3.genbank.mrna.xeno.load = no
priPac3.genbank.est.native.load = yes
priPac3.genbank.est.native.loadDesc = no
priPac3.downloadDir = priPac3
priPac3.perChromTables = no

# priPac1 (P. pacificus)
priPac1.serverGenome = /hive/data/genomes/priPac1/priPac1.2bit
priPac1.ooc = /hive/data/genomes/priPac1/11.ooc
priPac1.lift = /hive/data/genomes/priPac1/jkStuff/priPac1.supercontigs.lift
priPac1.align.unplacedChroms = chrUn
priPac1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
priPac1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
priPac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
priPac1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
priPac1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
priPac1.refseq.mrna.native.load = no
priPac1.refseq.mrna.xeno.load  = yes
priPac1.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
priPac1.genbank.est.native.load = yes
priPac1.genbank.est.native.loadDesc = no
priPac1.downloadDir = priPac1
priPac1.perChromTables = no

# proCap1 (Rock hyrax)
proCap1.serverGenome = /hive/data/genomes/proCap1/proCap1.2bit
proCap1.ooc = /hive/data/genomes/proCap1/jkStuff/proCap1.11.ooc
proCap1.lift = no
proCap1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
proCap1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
proCap1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
proCap1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
proCap1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
proCap1.refseq.mrna.native.load = no
proCap1.refseq.mrna.xeno.load = yes
proCap1.genbank.mrna.xeno.load = no
proCap1.genbank.est.native.load = no
proCap1.downloadDir = proCap1
proCap1.perChromTables = no

# pteVam1 (megabat)
pteVam1.serverGenome = /hive/data/genomes/pteVam1/pteVam1.2bit
pteVam1.ooc = /hive/data/genomes/pteVam1/jkStuff/pteVam1.11.ooc
pteVam1.lift = no
pteVam1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
pteVam1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
pteVam1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
pteVam1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
pteVam1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
pteVam1.refseq.mrna.native.load = no
pteVam1.refseq.mrna.xeno.load = yes
pteVam1.genbank.mrna.xeno.load = no
pteVam1.genbank.est.native.load = no
pteVam1.downloadDir = pteVam1
pteVam1.perChromTables = no

# rouAeg1 Rousettus aegyptiacus (Egyptian rousette (fruit bat))
rouAeg1.serverGenome = /hive/data/genomes/rouAeg1/rouAeg1.2bit
rouAeg1.ooc = /hive/data/genomes/rouAeg1/jkStuff/rouAeg1.11.ooc
rouAeg1.lift = no
rouAeg1.perChromTables = no
rouAeg1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
rouAeg1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
rouAeg1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
rouAeg1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
rouAeg1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
rouAeg1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
# refseq.mrna native and xeno are default yes
# genbank.mrna and genbank.est native are default yes, the xeno is default no
rouAeg1.refseq.mrna.native.load = no
rouAeg1.genbank.est.native.load = no
rouAeg1.downloadDir = rouAeg1

# saiBol1 (squirrel monkey)
saiBol1.serverGenome = /hive/data/genomes/saiBol1/saiBol1.2bit
saiBol1.ooc = /hive/data/genomes/saiBol1/jkStuff/saiBol1.11.ooc
saiBol1.lift = no
saiBol1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
saiBol1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
saiBol1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
saiBol1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
saiBol1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
saiBol1.refseq.mrna.native.load = no
saiBol1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
saiBol1.genbank.mrna.xeno.load = yes
saiBol1.genbank.est.native.load = no
saiBol1.downloadDir = saiBol1
saiBol1.perChromTables = no

# sorAra2 (common shrew)
sorAra2.serverGenome = /hive/data/genomes/sorAra2/sorAra2.2bit
sorAra2.ooc = /hive/data/genomes/sorAra2/jkStuff/sorAra2.11.ooc
sorAra2.lift = no
sorAra2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
sorAra2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
sorAra2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
sorAra2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
sorAra2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
sorAra2.refseq.mrna.native.load = no
sorAra2.refseq.mrna.xeno.load = yes
sorAra2.genbank.mrna.xeno.load = no
sorAra2.genbank.est.native.load = no
sorAra2.downloadDir = sorAra2
sorAra2.perChromTables = no

# sorAra1 (common shrew)
sorAra1.serverGenome = /hive/data/genomes/sorAra1/sorAra1.2bit
sorAra1.ooc = /hive/data/genomes/sorAra1/jkStuff/sorAra1.11.ooc
sorAra1.lift = no
sorAra1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
sorAra1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
sorAra1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
sorAra1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
sorAra1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
sorAra1.refseq.mrna.native.load = no
sorAra1.refseq.mrna.xeno.load = yes
sorAra1.genbank.mrna.xeno.load = no
sorAra1.genbank.est.native.load = no
sorAra1.downloadDir = sorAra1
sorAra1.perChromTables = no

# speTri2 (13-lined ground squirrel)
speTri2.serverGenome = /hive/data/genomes/speTri2/speTri2.2bit
speTri2.ooc = /hive/data/genomes/speTri2/jkStuff/speTri2.11.ooc
speTri2.lift = no
speTri2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
speTri2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
speTri2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
speTri2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
speTri2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
speTri2.refseq.mrna.native.load = no
speTri2.refseq.mrna.xeno.load = yes
speTri2.genbank.mrna.xeno.load = no
speTri2.genbank.est.native.load = yes
speTri2.downloadDir = speTri2
speTri2.perChromTables = no

# tarSyr2 (Tarsier)
tarSyr2.serverGenome = /hive/data/genomes/tarSyr2/tarSyr2.2bit
tarSyr2.ooc = /hive/data/genomes/tarSyr2/jkStuff/tarSyr2.11.ooc
tarSyr2.lift = no
tarSyr2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
tarSyr2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
tarSyr2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
tarSyr2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
tarSyr2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
tarSyr2.refseq.mrna.native.load = no
tarSyr2.refseq.mrna.xeno.load = yes
tarSyr2.genbank.mrna.xeno.load = no
tarSyr2.genbank.est.native.load = no
tarSyr2.downloadDir = tarSyr2
tarSyr2.perChromTables = no

# tarSyr1 (Tarsier)
tarSyr1.serverGenome = /hive/data/genomes/tarSyr1/tarSyr1.2bit
tarSyr1.ooc = /hive/data/genomes/tarSyr1/tarSyr1.11.ooc
tarSyr1.lift = no
tarSyr1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
tarSyr1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
tarSyr1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
tarSyr1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
tarSyr1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
tarSyr1.refseq.mrna.native.load = no
tarSyr1.refseq.mrna.xeno.load = yes
tarSyr1.genbank.mrna.xeno.load = no
tarSyr1.genbank.est.native.load = yes
tarSyr1.downloadDir = tarSyr1
tarSyr1.perChromTables = no

# tupChi1 (Chinese shrew)
tupChi1.serverGenome = /hive/data/genomes/tupChi1/tupChi1.2bit
tupChi1.ooc = /hive/data/genomes/tupChi1/jkStuff/tupChi1.11.ooc
tupChi1.lift = no
tupChi1.perChromTables = no
tupChi1.downloadDir = tupChi1
tupChi1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
tupChi1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
tupChi1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
tupChi1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
tupChi1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# the defaults: genbank.mrna.native.load, yes genbank.est.native.load yes
# refseq.mrna.native.load yes, refseq.mrna.xeno.load yes

# tupBel1 (common shrew)
tupBel1.serverGenome = /hive/data/genomes/tupBel1/tupBel1.2bit
tupBel1.ooc = /hive/data/genomes/tupBel1/tupBel1.11.ooc
tupBel1.lift = /hive/data/genomes/tupBel1/jkStuff/tupBel1.nonBridged.lift
tupBel1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
tupBel1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
tupBel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
tupBel1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
tupBel1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
tupBel1.refseq.mrna.native.load = no
tupBel1.refseq.mrna.xeno.load = yes
tupBel1.genbank.mrna.xeno.load = no
tupBel1.genbank.est.native.load = yes
tupBel1.downloadDir = tupBel1
tupBel1.perChromTables = no

# vicPac2 (alpaca)
vicPac2.serverGenome = /hive/data/genomes/vicPac2/vicPac2.2bit
vicPac2.ooc = /hive/data/genomes/vicPac2/jkStuff/vicPac2.11.ooc
vicPac2.lift = no
vicPac2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
vicPac2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
vicPac2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
vicPac2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
vicPac2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
vicPac2.downloadDir = vicPac2
vicPac2.perChromTables = no

# vicPac1 (alpaca)
vicPac1.serverGenome = /hive/data/genomes/vicPac1/vicPac1.2bit
vicPac1.ooc = /hive/data/genomes/vicPac1/jkStuff/vicPac1.11.ooc
vicPac1.lift = no
vicPac1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
vicPac1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
vicPac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
vicPac1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
vicPac1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
vicPac1.refseq.mrna.native.load = no
vicPac1.refseq.mrna.xeno.load = yes
vicPac1.genbank.mrna.native.load = no
vicPac1.genbank.mrna.xeno.load = no
vicPac1.genbank.est.native.load = yes
vicPac1.downloadDir = vicPac1
vicPac1.perChromTables = no

# balAcu1 (minke whale)
balAcu1.serverGenome = /hive/data/genomes/balAcu1/balAcu1.2bit
balAcu1.ooc = /hive/data/genomes/balAcu1/jkStuff/balAcu1.11.ooc
balAcu1.lift = no
balAcu1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
balAcu1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
balAcu1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
balAcu1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
balAcu1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
balAcu1.refseq.mrna.native.load = no
balAcu1.refseq.mrna.xeno.load = yes
balAcu1.genbank.mrna.xeno.load = no
balAcu1.genbank.est.native.load = no
balAcu1.genbank.mrna.native.load = no
balAcu1.genbank.mrna.native.loadDesc = no
balAcu1.downloadDir = balAcu1
balAcu1.perChromTables = no

# orcOrc1 (killer whale)
orcOrc1.serverGenome = /hive/data/genomes/orcOrc1/orcOrc1.2bit
orcOrc1.ooc = /hive/data/genomes/orcOrc1/jkStuff/orcOrc1.11.ooc
orcOrc1.lift = no
orcOrc1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
orcOrc1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
orcOrc1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
orcOrc1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
orcOrc1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
orcOrc1.refseq.mrna.native.load = no
orcOrc1.refseq.mrna.xeno.load = yes
orcOrc1.genbank.mrna.xeno.load = no
orcOrc1.genbank.est.native.load = no
orcOrc1.genbank.mrna.native.load = no
orcOrc1.genbank.mrna.native.loadDesc = no
orcOrc1.downloadDir = orcOrc1
orcOrc1.perChromTables = no
# refseq.mrna native and xeno are default yes
# genbank.mrna and genbank.est native are default yes, the xeno is default no
orcOrc1.genbank.est.native.load = no

# calMil1 (Elephant shark)
calMil1.serverGenome = /hive/data/genomes/calMil1/calMil1.2bit
calMil1.ooc = /hive/data/genomes/calMil1/jkStuff/calMil1.11.ooc
calMil1.lift = no
calMil1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
calMil1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
calMil1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
calMil1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
calMil1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
calMil1.refseq.mrna.native.load = no
calMil1.refseq.mrna.xeno.load = yes
calMil1.genbank.mrna.xeno.load = no
calMil1.genbank.est.native.load = yes
calMil1.genbank.mrna.native.load = yes
calMil1.genbank.mrna.native.loadDesc = no
calMil1.downloadDir = calMil1
calMil1.perChromTables = no

# caePb2 (C. brenneri)
caePb2.serverGenome = /hive/data/genomes/caePb2/caePb2.2bit
caePb2.ooc = /hive/data/genomes/caePb2/11.ooc
caePb2.lift = /hive/data/genomes/caePb2/jkStuff/caePb2.supercontigs.lift
caePb2.align.unplacedChroms = chrUn
caePb2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
caePb2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
caePb2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
caePb2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
caePb2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
caePb2.refseq.mrna.native.load = no
caePb2.refseq.mrna.xeno.load  = yes
caePb2.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
caePb2.genbank.mrna.xeno.load = yes
caePb2.genbank.est.native.load = yes
caePb2.genbank.est.native.loadDesc = no
caePb2.downloadDir = caePb2
caePb2.perChromTables = no

# caePb1 (C. brenneri aka C. PB2801)
caePb1.serverGenome = /hive/data/genomes/caePb1/caePb1.2bit
caePb1.ooc = /hive/data/genomes/caePb1/11.ooc
caePb1.lift = /hive/data/genomes/caePb1/jkStuff/caePb1.supercontigs.lift
caePb1.align.unplacedChroms = chrUn
caePb1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
caePb1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
caePb1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
caePb1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
caePb1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
caePb1.refseq.mrna.native.load = no
caePb1.refseq.mrna.xeno.load  = yes
caePb1.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
caePb1.genbank.est.native.load = no
caePb1.genbank.est.native.loadDesc = no
caePb1.downloadDir = caePb1
caePb1.perChromTables = no

# caeRem3 (C. remanei)
caeRem3.serverGenome = /hive/data/genomes/caeRem3/caeRem3.2bit
caeRem3.ooc = /hive/data/genomes/caeRem3/11.ooc
caeRem3.lift = /hive/data/genomes/caeRem3/downloads/caeRem3.chrUn.lift
caeRem3.align.unplacedChroms = chrUn
caeRem3.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
caeRem3.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
caeRem3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
caeRem3.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
caeRem3.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
caeRem3.refseq.mrna.native.load = no
caeRem3.refseq.mrna.xeno.load  = yes
caeRem3.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
caeRem3.genbank.mrna.xeno.load = yes
caeRem3.genbank.est.native.load = yes
caeRem3.genbank.est.native.loadDesc = no
caeRem3.downloadDir = caeRem3
caeRem3.perChromTables = no

# caeRem2 (C. remanei)
caeRem2.serverGenome = /hive/data/genomes/caeRem2/caeRem2.2bit
caeRem2.ooc = /hive/data/genomes/caeRem2/11.ooc
caeRem2.lift = /hive/data/genomes/caeRem2/jkStuff/caeRem2.chrUn.lift
caeRem2.align.unplacedChroms = chrUn
caeRem2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
caeRem2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
caeRem2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
caeRem2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
caeRem2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
caeRem2.refseq.mrna.native.load = no
caeRem2.refseq.mrna.xeno.load  = yes
caeRem2.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
caeRem2.genbank.est.native.load = yes
caeRem2.genbank.est.native.loadDesc = no
caeRem2.downloadDir = caeRem2
caeRem2.perChromTables = no

# caeJap1 (C. japonica)
caeJap1.serverGenome = /hive/data/genomes/caeJap1/caeJap1.2bit
caeJap1.ooc = /hive/data/genomes/caeJap1/11.ooc
caeJap1.lift = /hive/data/genomes/caeJap1/jkStuff/caeJap1.chrUn.lift
caeJap1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
caeJap1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
caeJap1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
caeJap1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
caeJap1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
caeJap1.refseq.mrna.native.load = yes
caeJap1.refseq.mrna.xeno.load  = yes
caeJap1.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
caeJap1.genbank.mrna.xeno.load = yes
caeJap1.genbank.est.native.load = yes
caeJap1.genbank.est.native.loadDesc = no
caeJap1.downloadDir = caeJap1
caeJap1.perChromTables = no

# Marmoset - GCF_009663435.1 - Callithrix_jacchus_cj1700_1.1
calJac4.serverGenome = /hive/data/genomes/calJac4/calJac4.2bit
calJac4.ooc = /hive/data/genomes/calJac4/jkStuff/calJac4.11.ooc
calJac4.lift = /hive/data/genomes/calJac4/jkStuff/calJac4.gaps.lft
calJac4.perChromTables = no
calJac4.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
calJac4.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
calJac4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
calJac4.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
calJac4.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
calJac4.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
calJac4.downloadDir = calJac4
calJac4.refseq.mrna.native.load  = yes
calJac4.refseq.mrna.xeno.load = yes
calJac4.refseq.mrna.xeno.loadDesc  = yes
calJac4.genbank.mrna.xeno.load  = yes
# calJac4.upstreamGeneTbl = ensGene
# calJac4.upstreamMaf = multiz13way /hive/data/genomes/calJac4/bed/multiz13way/species.list

# Marmoset
calJac3.serverGenome = /hive/data/genomes/calJac3/calJac3.2bit
calJac3.ooc = /hive/data/genomes/calJac3/calJac3.11.ooc
calJac3.lift = no
calJac3.perChromTables = no
calJac3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
calJac3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
calJac3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
calJac3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
calJac3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
calJac3.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
calJac3.downloadDir = calJac3
calJac3.refseq.mrna.native.load  = yes
calJac3.refseq.mrna.xeno.load = yes
calJac3.refseq.mrna.xeno.loadDesc  = yes
calJac3.genbank.mrna.xeno.load  = yes
calJac3.upstreamGeneTbl = ensGene
calJac3.upstreamMaf = multiz13way /hive/data/genomes/calJac3/bed/multiz13way/species.list

# Marmoset
calJac1.serverGenome = /hive/data/genomes/calJac1/calJac1.2bit
calJac1.ooc = /hive/data/genomes/calJac1/11.ooc
calJac1.lift = no
calJac1.perChromTables = no
calJac1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
calJac1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
calJac1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
calJac1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
calJac1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
calJac1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
calJac1.downloadDir = calJac1
calJac1.refseq.mrna.native.load  = yes
calJac1.refseq.mrna.xeno.load = yes
calJac1.refseq.mrna.xeno.loadDesc  = yes
calJac1.upstreamGeneTbl = xenoRefGene
calJac1.upstreamMaf = multiz9way /hive/data/genomes/calJac1/bed/multiz9way/species.list

# danRer3 (zebrafish)
# Lift file partitions unplaced sequence pseudo-chroms
danRer3.serverGenome = /hive/data/genomes/danRer3/danRer3.2bit
danRer3.ooc = /hive/data/genomes/danRer3/danRer3_11.ooc
danRer3.align.unplacedChroms = chrNA,chrUn
danRer3.lift = /hive/data/genomes/danRer3/liftSupertoChrom/liftNAandUnScaffoldsToChrom.lft
danRer3.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
danRer3.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
danRer3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
danRer3.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
danRer3.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
danRer3.downloadDir = danRer3
danRer3.mgc = yes
danRer3.upstreamGeneTbl = refGene
danRer3.upstreamMaf = multiz5way /hive/data/genomes/danRer3/bed/multiz5way/species.list

# danRer4 (zebrafish)
# Lift file partitions unplaced sequence pseudo-chroms
danRer4.serverGenome = /hive/data/genomes/danRer4/danRer4.2bit
danRer4.ooc = /hive/data/genomes/danRer4/danRer4_11.ooc
danRer4.lift = /hive/data/genomes/danRer4/jkStuff/liftAll.lft
danRer4.align.unplacedChroms = chrNA_random,chrUn_random
danRer4.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
danRer4.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
danRer4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
danRer4.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
danRer4.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
danRer4.downloadDir = danRer4
danRer4.mgc = yes
danRer4.upstreamGeneTbl = refGene
danRer4.upstreamMaf = multiz7way /hive/data/genomes/danRer4/bed/multiz7way/species.lst

# danRer5 (zebrafish)
danRer5.serverGenome = /hive/data/genomes/danRer5/danRer5.2bit
danRer5.ooc = /hive/data/genomes/danRer5/danRer5_11.ooc
danRer5.lift = /hive/data/genomes/danRer5/jkStuff/nonBridgedGap.lft
danRer5.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
danRer5.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
danRer5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
danRer5.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
danRer5.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
danRer5.downloadDir = danRer5
danRer5.perChromTables = no
danRer5.mgc = yes
danRer5.orfeome = yes
danRer5.upstreamGeneTbl = refGene

# danRer6 (zebrafish)
danRer6.serverGenome = /hive/data/genomes/danRer6/danRer6.2bit
danRer6.ooc = /hive/data/genomes/danRer6/11.ooc
danRer6.lift = /hive/data/genomes/danRer6/jkStuff/danRer6.unBridged.lift
danRer6.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
danRer6.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
danRer6.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
danRer6.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
danRer6.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
danRer6.genbank.mrna.xeno.load  = yes
danRer6.downloadDir = danRer6
danRer6.perChromTables = no
danRer6.refseq.mrna.xeno.load  = yes
danRer6.mgc = yes
danRer6.orfeome = yes
danRer6.upstreamGeneTbl = refGene
danRer6.upstreamMaf = multiz6way /hive/data/genomes/danRer6/bed/multiz6way/species.lst

# danRer7 (zebrafish)
danRer7.serverGenome = /hive/data/genomes/danRer7/danRer7.2bit
danRer7.ooc = /hive/data/genomes/danRer7/danRer7.11.ooc
danRer7.lift = no
danRer7.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
danRer7.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
danRer7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
danRer7.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
danRer7.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
danRer7.genbank.mrna.xeno.load  = yes
danRer7.downloadDir = danRer7
danRer7.perChromTables = no
danRer7.refseq.mrna.xeno.load  = yes
danRer7.mgc = yes
danRer7.orfeome = yes
danRer7.upstreamGeneTbl = ensGene
danRer7.upstreamMaf = multiz8way /hive/data/genomes/danRer7/bed/multiz8way/species.lst

# danRer10 (zebrafish)
danRer10.serverGenome = /hive/data/genomes/danRer10/danRer10.2bit
danRer10.ooc = /hive/data/genomes/danRer10/jkStuff/danRer10.11.ooc
danRer10.lift = no
danRer10.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
danRer10.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
danRer10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
danRer10.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
danRer10.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
danRer10.genbank.mrna.xeno.load  = yes
danRer10.downloadDir = danRer10
danRer10.perChromTables = no
danRer10.refseq.mrna.xeno.load  = yes
danRer10.mgc = yes
danRer10.orfeome = yes
# danRer10.upstreamGeneTbl = ensGene
# danRer10.upstreamMaf = multiz8way /hive/data/genomes/danRer10/bed/multiz8way/species.lst

# danRer11 (zebrafish)
danRer11.serverGenome = /hive/data/genomes/danRer11/danRer11.2bit
danRer11.ooc = /hive/data/genomes/danRer11/jkStuff/danRer11.11.ooc
danRer11.lift = /hive/data/genomes/danRer11/jkStuff/nonBridged.lft
danRer11.perChromTables = no
danRer11.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
danRer11.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
danRer11.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
danRer11.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
danRer11.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults are fine: genbank.mrna.native refseq.mrna.native refseq.mrna.xeno yes
# and genbank.est.native
danRer11.genbank.mrna.xeno.load  = yes
danRer11.refseq.mrna.xeno.load  = yes
danRer11.downloadDir = danRer11
# danRer11.upstreamGeneTbl = refGene
# danRer11.upstreamMaf = multiz7way
# /hive/data/genomes/danRer10/bed/multiz7way/species.lst

# ci1 (Ciona intestinalis)
ci1.serverGenome = /hive/data/genomes/ci1/nib/Scaffold*.nib
ci1.ooc = no
ci1.maxIntron = 20000
ci1.lift = no
ci1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ci1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ci1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ci1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ci1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
ci1.refseq.mrna.native.load = yes
ci1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
ci1.genbank.mrna.xeno.load = yes
ci1.downloadDir = ci1
ci1.perChromTables = no

# ci2 (Ciona intestinalis)
ci2.serverGenome = /hive/data/genomes/ci2/ci2.2bit
ci2.ooc = /hive/data/genomes/ci2/11.ooc
ci2.maxIntron = 20000
ci2.lift = no
ci2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
ci2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
ci2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
ci2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
ci2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
ci2.refseq.mrna.native.load = yes
ci2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
ci2.genbank.mrna.xeno.load = yes
ci2.downloadDir = ci2
ci2.perChromTables = no

# ci3 (Ciona intestinalis)
ci3.serverGenome = /hive/data/genomes/ci3/ci3.2bit
ci3.ooc = /hive/data/genomes/ci3/jkStuff/ci3.11.ooc
ci3.maxIntron = 20000
ci3.lift = no
ci3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
ci3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
ci3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
ci3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
ci3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# refseq.mrna native and xeno are default yes
# genbank.mrna and genbank.est native are default yes, the xeno is default no
ci3.downloadDir = ci3
ci3.perChromTables = no

# strPur1 (S. purpuratus)
#   302 genbank mRNA
#   219 refseq mRNA
# 89289 genbank EST
strPur1.serverGenome = /hive/data/genomes/strPur1/strPur1.2bit
strPur1.ooc = /hive/data/genomes/strPur1/11.ooc
strPur1.lift = no
strPur1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
strPur1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
strPur1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
strPur1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
strPur1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
strPur1.refseq.mrna.native.load = yes
strPur1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
strPur1.genbank.est.native.load = no
strPur1.downloadDir = strPur1
strPur1.perChromTables = no


# strPur2 (S. purpuratus)
strPur2.serverGenome = /hive/data/genomes/strPur2/strPur2.2bit
strPur2.ooc = /hive/data/genomes/strPur2/11.ooc
strPur2.lift = no
strPur2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
strPur2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
strPur2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
strPur2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
strPur2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
strPur2.refseq.mrna.native.load = yes
strPur2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
strPur2.genbank.mrna.xeno.load = yes
strPur2.genbank.est.native.load = yes
strPur2.downloadDir = strPur2
strPur2.perChromTables = no


# strPur4 (S. purpuratus)
strPur4.serverGenome = /hive/data/genomes/strPur4/strPur4.2bit
strPur4.ooc = /hive/data/genomes/strPur4/strPur4.11.ooc
strPur4.lift = no
strPur4.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
strPur4.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
strPur4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
strPur4.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
strPur4.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
strPur4.refseq.mrna.native.load = yes
strPur4.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
strPur4.genbank.est.native.load = yes
strPur4.downloadDir = strPur4
strPur4.perChromTables = no

# canFam1 (dog)
canFam1.serverGenome = /hive/data/genomes/canFam1/nib/chr*.nib
canFam1.ooc = /hive/data/genomes/canFam1/11.ooc
canFam1.align.unplacedChroms = chrUn
canFam1.lift = /hive/data/genomes/canFam1/jkStuff/liftAll.lft
canFam1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
canFam1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
canFam1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
canFam1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
canFam1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
canFam1.refseq.mrna.native.load = yes
canFam1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
canFam1.downloadDir = canFam1
canFam1.upstreamGeneTbl = ensGene

# canFam2 (dog)
canFam2.serverGenome = /hive/data/genomes/canFam2/nib/chr*.nib
canFam2.ooc = /hive/data/genomes/canFam2/11.ooc
canFam2.lift = /hive/data/genomes/canFam2/jkStuff/liftAll.lft
canFam2.align.unplacedChroms = chrUn
canFam2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
canFam2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
canFam2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
canFam2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
canFam2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
canFam2.refseq.mrna.native.load = yes
canFam2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
canFam2.genbank.mrna.xeno.load = yes
canFam2.downloadDir = canFam2
canFam2.upstreamGeneTbl = refGene
canFam2.upstreamMaf = multiz4way /hive/data/genomes/canFam2/bed/multiz4way/species.lst

# canFam3 (dog)
canFam3.serverGenome = /hive/data/genomes/canFam3/canFam3.2bit
canFam3.ooc = /hive/data/genomes/canFam3/jkStuff/canFam3.11.ooc
canFam3.lift = /hive/data/genomes/canFam3/jkStuff/canFam3.nonBridged.lift
canFam3.align.unplacedChroms = chr*
canFam3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
canFam3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
canFam3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
canFam3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
canFam3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
canFam3.refseq.mrna.native.load = yes
canFam3.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
canFam3.genbank.mrna.xeno.load = yes
canFam3.downloadDir = canFam3
canFam3.upstreamGeneTbl = refGene
canFam3.perChromTables = no

# canFam4 (German shepard - GCA_011100685.1 - UU_Cfam_GSD_1.0)
canFam4.serverGenome = /hive/data/genomes/canFam4/canFam4.2bit
canFam4.ooc = /hive/data/genomes/canFam4/jkStuff/canFam4.11.ooc
canFam4.lift = /hive/data/genomes/canFam4/jkStuff/canFam4.nonBridged.lft
canFam4.align.unplacedChroms = chrUn_*
canFam4.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
canFam4.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
canFam4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
canFam4.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
canFam4.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
canFam4.refseq.mrna.native.load = yes
canFam4.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
canFam4.genbank.mrna.xeno.load = yes
canFam4.downloadDir = canFam4
canFam4.upstreamGeneTbl = refGene
canFam4.perChromTables = no

# canFam5 (Great Dane - GCA_005444595.1 - UMICH_Zoey_3.1) 
canFam5.serverGenome = /hive/data/genomes/canFam5/canFam5.2bit
canFam5.ooc = /hive/data/genomes/canFam5/jkStuff/canFam5.11.ooc
canFam5.lift = /hive/data/genomes/canFam5/jkStuff/canFam5.5Kgaps.lft
canFam5.align.unplacedChroms = chrUn_*
canFam5.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
canFam5.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
canFam5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
canFam5.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
canFam5.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
canFam5.refseq.mrna.native.load = yes
canFam5.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
canFam5.genbank.mrna.xeno.load = yes
canFam5.downloadDir = canFam5
canFam5.upstreamGeneTbl = refGene
canFam5.perChromTables = no

# canFam6 (GCF_000002285.5 Dog10K Boxer Tasha)
canFam6.serverGenome = /hive/data/genomes/canFam6/canFam6.2bit
canFam6.ooc = /hive/data/genomes/canFam6/jkStuff/canFam6.11.ooc
canFam6.lift = /hive/data/genomes/canFam6/jkStuff/canFam6.gaps.lft
canFam6.align.unplacedChroms = chrUn_*
canFam6.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
canFam6.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
canFam6.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
canFam6.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
canFam6.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
canFam6.refseq.mrna.native.load = yes
canFam6.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
canFam6.genbank.mrna.xeno.load = yes
canFam6.downloadDir = canFam6
canFam6.upstreamGeneTbl = refGene
canFam6.perChromTables = no

# ailMel1 (panda)
ailMel1.serverGenome = /hive/data/genomes/ailMel1/ailMel1.2bit
ailMel1.lift = no
ailMel1.ooc = /hive/data/genomes/ailMel1/ailMel1.11.ooc
ailMel1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ailMel1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ailMel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ailMel1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ailMel1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
ailMel1.refseq.mrna.native.load = no
ailMel1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
ailMel1.genbank.mrna.xeno.load = yes
ailMel1.downloadDir = ailMel1
ailMel1.perChromTables = no
ailMel1.upstreamGeneTbl = ensGene

# droYak1 (D. yakuba)
droYak1.serverGenome = /hive/data/genomes/droYak1/nib/chr*.nib
droYak1.ooc = /hive/data/genomes/droYak1/11.ooc
droYak1.lift = /hive/data/genomes/droYak1/jkStuff/liftAll.lft
droYak1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droYak1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droYak1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droYak1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droYak1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droYak1.refseq.mrna.native.load = no
droYak1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
droYak1.downloadDir = droYak1

# anoGam3 (A. gambiae)
anoGam3.serverGenome = /hive/data/genomes/anoGam3/anoGam3.2bit
anoGam3.ooc = /hive/data/genomes/anoGam3/jkStuff/anoGam3.11.ooc
anoGam3.lift = /hive/data/genomes/anoGam3/jkStuff/nonBridged.lft
anoGam3.perChromTables = no
anoGam3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
anoGam3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
anoGam3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
anoGam3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
anoGam3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# anoGam1 had genbank.mrna.xeno.load as yes
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
anoGam3.genbank.mrna.xeno.load = yes
anoGam3.downloadDir = anoGam3

# anoGam1 (A. gambiae)
anoGam1.serverGenome = /hive/data/genomes/anoGam1/nib/chr*.nib
anoGam1.ooc = /hive/data/genomes/anoGam1/11.ooc
anoGam1.lift = /hive/data/genomes/anoGam1/jkStuff/liftAll.lft
anoGam1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
anoGam1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
anoGam1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
anoGam1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
anoGam1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
anoGam1.refseq.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
anoGam1.genbank.mrna.xeno.load = yes
anoGam1.downloadDir = anoGam1

# dp2 (D. pseudoobscura)
dp2.serverGenome = /hive/data/genomes/dp2/nib/*.nib
dp2.ooc = /hive/data/genomes/dp2/11.ooc
dp2.lift = no
dp2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
dp2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
dp2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
dp2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
dp2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
dp2.refseq.mrna.native.load = no
dp2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dp2.downloadDir = dp2
dp2.perChromTables = no

# dp3 (D. pseudoobscura)
dp3.serverGenome = /hive/data/genomes/dp3/nib/*.nib
dp3.ooc = /hive/data/genomes/dp3/11.ooc
dp3.lift = /hive/data/genomes/dp3/jkStuff/liftAll.lft
dp3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
dp3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
dp3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
dp3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
dp3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
dp3.refseq.mrna.native.load = no
dp3.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dp3.genbank.est.native.load = yes
dp3.downloadDir = dp3

# tetNig2 (Tetraodon)
tetNig2.serverGenome = /hive/data/genomes/tetNig2/tetNig2.2bit
tetNig2.ooc = /hive/data/genomes/tetNig2/tetNig2.11.ooc
tetNig2.lift = /hive/data/genomes/tetNig2/tetNig2.contigs.lift
tetNig2.align.unplacedChroms = chr*_random
tetNig2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
tetNig2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
tetNig2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
tetNig2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
tetNig2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
tetNig2.downloadDir = tetNig2
tetNig2.genbank.est.native.load = no
tetNig2.genbank.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
tetNig2.genbank.mrna.xeno.load = yes
tetNig2.refseq.mrna.native.load = no
tetNig2.upstreamGeneTbl = ensGene

# tetNig1 (Tetraodon)
tetNig1.serverGenome = /hive/data/genomes/tetNig1/nib/chr*.nib
tetNig1.ooc = /hive/data/genomes/tetNig1/11.ooc
tetNig1.lift = /hive/data/genomes/tetNig1/jkStuff/liftAll.lft
tetNig1.align.unplacedChroms = chrUn_random
tetNig1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
tetNig1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
tetNig1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
tetNig1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
tetNig1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
tetNig1.downloadDir = tetNig1
tetNig1.genbank.est.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
tetNig1.refseq.mrna.native.load = no
tetNig1.upstreamGeneTbl = ensGene

# poeRet1 (guppy)
poeRet1.serverGenome = /hive/data/genomes/poeRet1/poeRet1.2bit
poeRet1.ooc = /hive/data/genomes/poeRet1/jkStuff/poeRet1.11.ooc
poeRet1.lift = /hive/data/genomes/poeRet1/jkStuff/poeRet1.nonBridged.lift
poeRet1.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
poeRet1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
poeRet1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
poeRet1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
poeRet1.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
poeRet1.refseq.mrna.native.load = no
poeRet1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
poeRet1.genbank.est.native.load = yes
poeRet1.downloadDir = poeRet1
poeRet1.perChromTables = no

# gasAcu1 (G. Aculeatus)
gasAcu1.serverGenome = /hive/data/genomes/gasAcu1/gasAcu1.2bit
gasAcu1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
gasAcu1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
gasAcu1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
gasAcu1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
gasAcu1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
gasAcu1.ooc = /hive/data/genomes/gasAcu1/11.ooc
gasAcu1.lift = /hive/data/genomes/gasAcu1/jkStuff/liftAll.lft
# DO NOT NEED genbank.mrna.xeno except for human, mouse
gasAcu1.genbank.mrna.xeno.load = yes
gasAcu1.downloadDir = gasAcu1
gasAcu1.upstreamGeneTbl = ensGene
gasAcu1.upstreamMaf = multiz8way /hive/data/genomes/gasAcu1/bed/multiz8way/species.lst

# chiLan1 (Chinchilla lanigera)
chiLan1.serverGenome = /hive/data/genomes/chiLan1/chiLan1.2bit
chiLan1.lift = no
chiLan1.perChromTables = no
chiLan1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
chiLan1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
chiLan1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
chiLan1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
chiLan1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
chiLan1.ooc = /hive/data/genomes/chiLan1/jkStuff/chiLan1.11.ooc
chiLan1.refseq.mrna.native.load = yes
chiLan1.refseq.mrna.xeno.load = yes
chiLan1.genbank.mrna.xeno.load = no
chiLan1.genbank.est.native.load = yes
chiLan1.downloadDir = chiLan1

# musFur1 (Ferret, Mustela putorius furo, taxId 9669)
musFur1.serverGenome = /hive/data/genomes/musFur1/musFur1.2bit
musFur1.ooc = /hive/data/genomes/musFur1/jkStuff/musFur1.11.ooc
musFur1.lift = no
musFur1.perChromTables = no
musFur1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
musFur1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
musFur1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
musFur1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
musFur1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
musFur1.refseq.mrna.native.load = yes
musFur1.refseq.mrna.xeno.load = yes
musFur1.genbank.mrna.xeno.load = no
musFur1.genbank.est.native.load = yes
musFur1.downloadDir = musFur1

# enhLutNer1 Enhydra lutris nereis (southern sea otter) (genbank assembly GCA_006410715.1)
enhLutNer1.serverGenome = /hive/data/genomes/enhLutNer1/enhLutNer1.2bit
enhLutNer1.ooc = /hive/data/genomes/enhLutNer1/jkStuff/enhLutNer1.11.ooc
enhLutNer1.lift = no
enhLutNer1.perChromTables = no
enhLutNer1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
enhLutNer1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
enhLutNer1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
enhLutNer1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
enhLutNer1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
enhLutNer1.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
enhLutNer1.downloadDir = enhLutNer1
enhLutNer1.refseq.mrna.native.load  = yes
enhLutNer1.refseq.mrna.xeno.load  = yes

# oryLat2 (Oryzias latipes - Medaka)
oryLat2.serverGenome = /hive/data/genomes/oryLat2/oryLat2.2bit
oryLat2.lift = /hive/data/genomes/oryLat2/jkStuff/liftAll.lft
oryLat2.perChromTables = no
oryLat2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
oryLat2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
oryLat2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
oryLat2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
oryLat2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
oryLat2.ooc = /hive/data/genomes/oryLat2/11.ooc
# DO NOT NEED genbank.mrna.xeno except for human, mouse
oryLat2.genbank.mrna.xeno.load = yes
oryLat2.refseq.mrna.native.load = yes
oryLat2.refseq.mrna.xeno.load = yes
oryLat2.downloadDir = oryLat2
oryLat2.upstreamGeneTbl = ensGene
oryLat2.upstreamMaf = multiz5way /hive/data/genomes/oryLat2/bed/multiz5way/species.list

# oryLat1 (Oryzias latipes - Medaka)
oryLat1.serverGenome = /hive/data/genomes/oryLat1/oryLat1.2bit
oryLat1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
oryLat1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
oryLat1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
oryLat1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
oryLat1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
oryLat1.ooc = /hive/data/genomes/oryLat1/11.ooc
oryLat1.lift = /hive/data/genomes/oryLat1/jkStuff/liftAll.lft
# DO NOT NEED genbank.mrna.xeno except for human, mouse
oryLat1.refseq.mrna.native.load = no
oryLat1.refseq.mrna.xeno.load = yes
oryLat1.downloadDir = oryLat1

# oviAri4 (sheep - Ovis aries - refseq GCF_000298735.2 - taxId 9940)
oviAri4.serverGenome = /hive/data/genomes/oviAri4/oviAri4.2bit
oviAri4.ooc = /hive/data/genomes/oviAri4/jkStuff/oviAri4.11.ooc
oviAri4.lift = no
oviAri4.perChromTables = no
oviAri4.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
oviAri4.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
oviAri4.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
oviAri4.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
oviAri4.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
oviAri4.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
oviAri4.downloadDir = oviAri4
# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
# yes: genbank.est.native.load refseq.mrna.native.load
# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
# yes: refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
# no: genbank.est.native.loadDesc genbank.est.xeno.load
# no: genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# have been doing this for chimp too:
oviAri4.genbank.mrna.xeno.load = no

# oviAri3 (Sheep)
oviAri3.serverGenome = /hive/data/genomes/oviAri3/oviAri3.2bit
oviAri3.ooc = /hive/data/genomes/oviAri3/jkStuff/oviAri3.11.ooc
oviAri3.lift = no
oviAri3.perChromTables = no
oviAri3.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
oviAri3.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
oviAri3.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
oviAri3.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
oviAri3.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
oviAri3.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
oviAri3.downloadDir = oviAri3
oviAri3.refseq.mrna.native.load  = yes
oviAri3.refseq.mrna.xeno.load = yes
oviAri3.refseq.mrna.xeno.loadDesc  = yes
oviAri3.genbank.mrna.xeno.load  = yes
oviAri3.upstreamGeneTbl = refGene

# oviAri1 (Sheep)
oviAri1.serverGenome = /hive/data/genomes/oviAri1/oviAri1.2bit
oviAri1.ooc = /hive/data/genomes/oviAri1/oviAri1.11.ooc
oviAri1.lift = no
oviAri1.perChromTables = no
oviAri1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
oviAri1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
oviAri1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
oviAri1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
oviAri1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
oviAri1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
oviAri1.downloadDir = oviAri1
oviAri1.refseq.mrna.native.load  = yes
oviAri1.refseq.mrna.xeno.load = yes
oviAri1.refseq.mrna.xeno.loadDesc  = yes
oviAri1.upstreamGeneTbl = refGene

# otoGar3 (bushbaby)
otoGar3.serverGenome = /hive/data/genomes/otoGar3/otoGar3.2bit
otoGar3.ooc = /hive/data/genomes/otoGar3/jkStuff/otoGar3.11.ooc
otoGar3.lift = no
otoGar3.perChromTables = no
otoGar3.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
otoGar3.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
otoGar3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
otoGar3.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
otoGar3.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
otoGar3.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
otoGar3.downloadDir = otoGar3
otoGar3.refseq.mrna.native.load  = no
otoGar3.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
otoGar3.genbank.mrna.xeno.load = yes
otoGar3.genbank.mrna.xeno.loadDesc = no
otoGar3.genbank.est.native.load = no

# susScr11 (pig)
susScr11.serverGenome = /hive/data/genomes/susScr11/susScr11.2bit
susScr11.ooc = /hive/data/genomes/susScr11/jkStuff/susScr11.11.ooc
susScr11.lift = /hive/data/genomes/susScr11/jkStuff/susScr11.nonBridged.lft
susScr11.perChromTables = no
susScr11.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
susScr11.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
susScr11.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
susScr11.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
susScr11.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
susScr11.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
susScr11.downloadDir = susScr11
susScr11.refseq.mrna.native.load  = yes
susScr11.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
susScr11.genbank.mrna.xeno.load = yes
susScr11.genbank.mrna.xeno.loadDesc = no
susScr11.genbank.est.native.load = yes
# susScr11.upstreamGeneTbl = ensGene
# susScr11.upstreamMaf = multiz12way
# /hive/data/genomes/susScr11/bed/multiz12way/species.list

# susScr3 (pig)
susScr3.serverGenome = /hive/data/genomes/susScr3/susScr3.2bit
susScr3.ooc = /hive/data/genomes/susScr3/jkStuff/susScr3.11.ooc
susScr3.lift = /hive/data/genomes/susScr3/jkStuff/susScr3.nonBridged.lift
susScr3.perChromTables = no
susScr3.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
susScr3.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
susScr3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
susScr3.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
susScr3.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
susScr3.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
susScr3.downloadDir = susScr3
susScr3.refseq.mrna.native.load  = yes
susScr3.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
susScr3.genbank.mrna.xeno.load = yes
susScr3.genbank.mrna.xeno.loadDesc = no
susScr3.genbank.est.native.load = yes
# susScr3.upstreamGeneTbl = ensGene
# susScr3.upstreamMaf = multiz12way
# /hive/data/genomes/susScr3/bed/multiz12way/species.list

# susScr2 (Pig)
susScr2.serverGenome = /hive/data/genomes/susScr2/susScr2.2bit
susScr2.ooc = /hive/data/genomes/susScr2/susScr2.11.ooc
susScr2.lift = /hive/data/genomes/susScr2/susScr2.nonBridged.lft
susScr2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
susScr2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
susScr2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
susScr2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
susScr2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
susScr2.downloadDir = susScr2
susScr2.genbank.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
susScr2.genbank.mrna.xeno.load = yes
susScr2.refseq.mrna.native.load = no
susScr2.upstreamGeneTbl = ensGene

# equCab3 (Equus caballus)
equCab3.serverGenome = /hive/data/genomes/equCab3/equCab3.2bit
equCab3.ooc = /hive/data/genomes/equCab3/jkStuff/equCab3.11.ooc
equCab3.lift = no
equCab3.downloadDir = equCab3
equCab3.perChromTables = no
equCab3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
equCab3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
equCab3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
equCab3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
equCab3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
# yes: genbank.est.native.load refseq.mrna.native.load
# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
# yes: refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
# no: genbank.est.native.loadDesc genbank.est.xeno.load
# no: genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# equCab3.upstreamGeneTbl = refGene
# equCab3.upstreamMaf = multiz6way /hive/data/genomes/equCab3/bed/multiz6way/species.list

# equCab2 (Equus caballus)
equCab2.serverGenome = /hive/data/genomes/equCab2/equCab2.2bit
equCab2.ooc = /hive/data/genomes/equCab2/equCab2.11.ooc
equCab2.lift = /hive/data/genomes/equCab2/jkStuff/equCab2.chrUn.lift
equCab2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
equCab2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
equCab2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
equCab2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
equCab2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
equCab2.align.unplacedChroms = chrUn
equCab2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
equCab2.genbank.mrna.xeno.load = yes
equCab2.downloadDir = equCab2
equCab2.upstreamGeneTbl = refGene
# equCab2.upstreamMaf = multiz6way /hive/data/genomes/equCab2/bed/multiz6way/species.list

# equCab1 (Equus caballus)
equCab1.serverGenome = /hive/data/genomes/equCab1/equCab1.2bit
equCab1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
equCab1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
equCab1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
equCab1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
equCab1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
equCab1.ooc = /hive/data/genomes/equCab1/11.ooc
equCab1.lift = /hive/data/genomes/equCab1/jkStuff/genbank.lft
equCab1.align.unplacedChroms = chrUn
# DO NOT NEED genbank.mrna.xeno except for human, mouse
equCab1.genbank.mrna.xeno.load = yes
equCab1.downloadDir = equCab1
equCab1.upstreamGeneTbl = refGene

# cerSim1 (Ceratotherium simum - White Rhino)
cerSim1.serverGenome = /hive/data/genomes/cerSim1/cerSim1.2bit
cerSim1.ooc = /hive/data/genomes/cerSim1/jkStuff/cerSim1.11.ooc
cerSim1.lift = no
cerSim1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
cerSim1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
cerSim1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
cerSim1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
cerSim1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
cerSim1.refseq.mrna.native.load = no
cerSim1.refseq.mrna.xeno.load = yes
cerSim1.genbank.mrna.xeno.load = no
cerSim1.genbank.est.native.load = no
cerSim1.downloadDir = cerSim1
cerSim1.perChromTables = no

# Nov 2017 (GSC) at Washington University (WashU) School of Medicine
#       Felis_catus_9.0
# felCat9 (Cat)
felCat9.serverGenome = /hive/data/genomes/felCat9/felCat9.2bit
felCat9.ooc = /hive/data/genomes/felCat9/jkStuff/felCat9.11.ooc
felCat9.lift = /hive/data/genomes/felCat9/jkStuff/felCat9.nonBridged.lft
felCat9.perChromTables = no
felCat9.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
felCat9.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
felCat9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
felCat9.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
felCat9.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
felCat9.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
felCat9.genbank.mrna.xeno.load  = yes
felCat9.downloadDir = felCat9
felCat9.refseq.mrna.native.load  = yes
felCat9.refseq.mrna.xeno.load = yes
felCat9.refseq.mrna.xeno.loadDesc  = yes
# felCat9.upstreamGeneTbl = refGene
# felCat9.upstreamMaf = multiz6way
# /hive/data/genomes/felCat9/bed/multiz6way/species.list

# Nov. 2014 International Cat Genome Sequencing Consortium Felis_catus_8.0
# felCat8 (Cat)
felCat8.serverGenome = /hive/data/genomes/felCat8/felCat8.2bit
felCat8.ooc = /hive/data/genomes/felCat8/jkStuff/felCat8.11.ooc
felCat8.lift = /hive/data/genomes/felCat8/jkStuff/felCat8.nonBridged.lift
felCat8.perChromTables = no
felCat8.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
felCat8.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
felCat8.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
felCat8.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
felCat8.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
felCat8.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
felCat8.genbank.mrna.xeno.load  = yes
felCat8.downloadDir = felCat8
felCat8.refseq.mrna.native.load  = yes
felCat8.refseq.mrna.xeno.load = yes
felCat8.refseq.mrna.xeno.loadDesc  = yes
# felCat8.upstreamGeneTbl = refGene
# felCat8.upstreamMaf = multiz6way /hive/data/genomes/felCat8/bed/multiz6way/species.list


# felCat5
felCat5.serverGenome = /hive/data/genomes/felCat5/felCat5.2bit
felCat5.ooc = /hive/data/genomes/felCat5/jkStuff/felCat5.11.ooc
felCat5.lift = /hive/data/genomes/felCat5/jkStuff/felCat5.nonBridged.lift
felCat5.perChromTables = no
felCat5.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
felCat5.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
felCat5.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
felCat5.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
felCat5.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
felCat5.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
felCat5.genbank.mrna.xeno.load  = yes
felCat5.downloadDir = felCat5
felCat5.refseq.mrna.native.load  = yes
felCat5.refseq.mrna.xeno.load = yes
felCat5.refseq.mrna.xeno.loadDesc  = yes
# felCat5.upstreamGeneTbl = refGene
# felCat5.upstreamMaf = multiz6way /hive/data/genomes/felCat5/bed/multiz6way/species.list

# felCat4
felCat4.serverGenome = /hive/data/genomes/felCat4/felCat4.2bit
felCat4.ooc = /hive/data/genomes/felCat4/felCat4.11.ooc
felCat4.lift = no
felCat4.perChromTables = no
felCat4.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
felCat4.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
felCat4.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
felCat4.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
felCat4.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
felCat4.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
felCat4.downloadDir = felCat4
felCat4.refseq.mrna.native.load  = yes
felCat4.refseq.mrna.xeno.load = yes
felCat4.refseq.mrna.xeno.loadDesc  = yes
felCat4.upstreamGeneTbl = refGene
felCat4.upstreamMaf = multiz6way /hive/data/genomes/felCat4/bed/multiz6way/species.list

# felCat3 (cat) 217790 scaffolds
felCat3.serverGenome = /hive/data/genomes/felCat3/felCat3.2bit
felCat3.ooc = /hive/data/genomes/felCat3/11.ooc
felCat3.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
felCat3.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
felCat3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
felCat3.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
felCat3.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
felCat3.lift = no
felCat3.refseq.mrna.xeno.load = yes
felCat3.downloadDir = felCat3
felCat3.perChromTables = no
felCat3.upstreamGeneTbl = ensGene
felCat3.upstreamMaf = multiz4way /hive/data/genomes/felCat3/bed/multiz4way/species.lst

# bisBis1 (Bison)  450182 contigs
bisBis1.serverGenome = /hive/data/genomes/bisBis1/bisBis1.2bit
bisBis1.ooc = /hive/data/genomes/bisBis1/jkStuff/bisBis1.11.ooc
bisBis1.lift = no
bisBis1.perChromTables = no
bisBis1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
bisBis1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
bisBis1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
bisBis1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
bisBis1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
bisBis1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
bisBis1.downloadDir = bisBis1
bisBis1.refseq.mrna.native.load  = yes
bisBis1.refseq.mrna.xeno.load = yes
bisBis1.refseq.mrna.xeno.loadDesc  = yes
bisBis1.genbank.mrna.native.load = no
bisBis1.genbank.mrna.native.loadDesc = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
bisBis1.genbank.mrna.xeno.load = no
bisBis1.genbank.mrna.xeno.loadDesc = no
bisBis1.genbank.est.native.load = no
bisBis1.genbank.est.native.loadDesc = no
# bisBis1.upstreamGeneTbl = ensGene

# bosTau2 (B. taurus) 30 chromosomes plus 98058 scaffolds
# Lift file partitions unplaced sequence pseudo-chroms
bosTau2.serverGenome = /hive/data/genomes/bosTau2/bosTau2.2bit
bosTau2.ooc = /hive/data/genomes/bosTau2/11.ooc
bosTau2.lift = /hive/data/genomes/bosTau2/downloads/chrBin0.lft
bosTau2.align.unplacedChroms = chrBin0
bosTau2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
bosTau2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
bosTau2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
bosTau2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
bosTau2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
bosTau2.refseq.mrna.native.load = yes
bosTau2.refseq.mrna.xeno.load = yes
bosTau2.downloadDir = bosTau2
bosTau2.perChromTables = no
bosTau2.mgc = yes
bosTau2.upstreamGeneTbl = refGene

# bosTau3 (B. taurus) 30 chromosomes plus 13045 scaffolds
bosTau3.serverGenome = /hive/data/genomes/bosTau3/bosTau3.2bit
bosTau3.ooc = /hive/data/genomes/bosTau3/11.ooc
bosTau3.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
bosTau3.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
bosTau3.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
bosTau3.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
bosTau3.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
bosTau3.lift = no
bosTau3.downloadDir = bosTau3
bosTau3.perChromTables = no
bosTau3.mgc = yes
bosTau3.upstreamGeneTbl = refGene

# bosTau4 (B. taurus) 31 chromosomes plus 11869 scaffolds
bosTau4.serverGenome = /hive/data/genomes/bosTau4/bosTau4.2bit
bosTau4.ooc = /hive/data/genomes/bosTau4/bosTau4.11.ooc
bosTau4.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
bosTau4.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
bosTau4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
bosTau4.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
bosTau4.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
bosTau4.lift = no
bosTau4.downloadDir = bosTau4
bosTau4.perChromTables = no
bosTau4.mgc = yes
bosTau4.upstreamGeneTbl = mgcGenes
bosTau4.upstreamMaf = multiz5way /hive/data/genomes/bosTau4/bed/multiz5way/species.list

# bosTau6 (Cow)
bosTau6.serverGenome = /hive/data/genomes/bosTau6/bosTau6.2bit
bosTau6.ooc = /hive/data/genomes/bosTau6/bosTau6.11.ooc
bosTau6.lift = no
bosTau6.perChromTables = no
bosTau6.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
bosTau6.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
bosTau6.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
bosTau6.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
bosTau6.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
bosTau6.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
bosTau6.downloadDir = bosTau6
bosTau6.refseq.mrna.native.load  = yes
bosTau6.refseq.mrna.xeno.load = yes
bosTau6.refseq.mrna.xeno.loadDesc  = yes
bosTau6.genbank.mrna.xeno.load  = yes
bosTau6.upstreamGeneTbl = refGene

# bosTau7 (Cow)
bosTau7.serverGenome = /hive/data/genomes/bosTau7/bosTau7.2bit
bosTau7.ooc = /hive/data/genomes/bosTau7/bosTau7.11.ooc
bosTau7.lift = no
bosTau7.perChromTables = no
bosTau7.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
bosTau7.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
bosTau7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
bosTau7.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
bosTau7.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
bosTau7.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
bosTau7.downloadDir = bosTau7
bosTau7.refseq.mrna.native.load  = yes
bosTau7.refseq.mrna.xeno.load = yes
bosTau7.refseq.mrna.xeno.loadDesc  = yes
bosTau7.genbank.mrna.xeno.load  = yes
bosTau7.upstreamGeneTbl = refGene

bosTau8.serverGenome = /hive/data/genomes/bosTau8/bosTau8.2bit
bosTau8.ooc = /hive/data/genomes/bosTau8/bosTau8.11.ooc
bosTau8.lift = no
bosTau8.perChromTables = no
bosTau8.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
bosTau8.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
bosTau8.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
bosTau8.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
bosTau8.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
bosTau8.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
bosTau8.downloadDir = bosTau8
bosTau8.refseq.mrna.native.load  = yes
bosTau8.refseq.mrna.xeno.load = yes
bosTau8.refseq.mrna.xeno.loadDesc  = yes
bosTau8.upstreamGeneTbl = refGene

# bosTau9 (cow - Bos taurus - refseq GCF_002263795.1 ARS-UCD1.2 - taxId 9913)
bosTau9.serverGenome = /hive/data/genomes/bosTau9/bosTau9.2bit
bosTau9.ooc = /hive/data/genomes/bosTau9/jkStuff/bosTau9.11.ooc
bosTau9.lift = no
bosTau9.perChromTables = no
bosTau9.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
bosTau9.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
bosTau9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
bosTau9.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
bosTau9.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
bosTau9.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
bosTau9.downloadDir = bosTau9
# bosTau9.upstreamGeneTbl = refGene
# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
# yes: genbank.est.native.load refseq.mrna.native.load
# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
# yes: refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
# no: genbank.est.native.loadDesc genbank.est.xeno.load
# no: genbank.est.xeno.loadDesc

# ambMex2 (Axolotl - Ambystoma mexicanum) GCA_002915635.2 - 30Gb total
ambMex2.serverGenome = /hive/data/genomes/ambMex2/ambMex2.2bit
ambMex2.ooc = /hive/data/genomes/ambMex2/jkStuff/ambMex2.11.ooc
ambMex2.lift = /hive/data/genomes/ambMex2/jkStuff/ambMex2.100baseGaps.lft
ambMex2.perChromTables = no
ambMex2.downloadDir = ambMex2
ambMex2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
ambMex2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
ambMex2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
ambMex2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
ambMex2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
ambMex2.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
# yes: genbank.est.native.load refseq.mrna.native.load
# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
# yes: refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
# no: genbank.est.native.loadDesc genbank.est.xeno.load
# no: genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# ambMex2.upstreamGeneTbl = ensGene
# ambMex2.upstreamMaf = multiz6way /hive/data/genomes/ambMex2/bed/multiz6way/species.list


# ambMex1 (Axolotl - Ambystoma mexicanum) 125724 scaffolds N50 3052786 - 30Gb total
ambMex1.serverGenome = /hive/data/genomes/ambMex1/ambMex1.2bit
ambMex1.ooc = /hive/data/genomes/ambMex1/jkStuff/ambMex1.11.ooc
ambMex1.lift = /hive/data/genomes/ambMex1/jkStuff/ambMex1.10Kgaps.lft
ambMex1.perChromTables = no
ambMex1.downloadDir = ambMex1
ambMex1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ambMex1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ambMex1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ambMex1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ambMex1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
ambMex1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
# yes: genbank.est.native.load refseq.mrna.native.load
# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
# yes: refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
# no: genbank.est.native.loadDesc genbank.est.xeno.load
# no: genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# ambMex1.upstreamGeneTbl = ensGene
# ambMex1.upstreamMaf = multiz6way /hive/data/genomes/ambMex1/bed/multiz6way/species.list

# nanPar1 (tibetan frog) 25187 scaffolds N50 1069101
nanPar1.serverGenome = /hive/data/genomes/nanPar1/nanPar1.2bit
nanPar1.ooc = /hive/data/genomes/nanPar1/jkStuff/nanPar1.11.ooc
nanPar1.lift = no
nanPar1.perChromTables = no
nanPar1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
nanPar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
nanPar1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
nanPar1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
nanPar1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
nanPar1.downloadDir = nanPar1
nanPar1.refseq.mrna.native.load  = no
nanPar1.refseq.mrna.xeno.load = yes
nanPar1.refseq.mrna.xeno.loadDesc  = yes
nanPar1.genbank.mrna.native.load = no
nanPar1.genbank.mrna.native.loadDesc = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
nanPar1.genbank.est.native.load = no
nanPar1.genbank.est.native.loadDesc = no
# nanPar1.upstreamGeneTbl = ensGene

# xenLae2 'Xenopus laevis' 19 chroms + 108014 contigs
xenLae2.serverGenome = /hive/data/genomes/xenLae2/xenLae2.2bit
xenLae2.ooc = /hive/data/genomes/xenLae2/jkStuff/xenLae2.11.ooc
xenLae2.lift = no
xenLae2.perChromTables = no
xenLae2.downloadDir = xenLae2
# xenLae2.mgc = yes
xenLae2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
xenLae2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
xenLae2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
xenLae2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
xenLae2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# xenLae2.upstreamGeneTbl = ensGene
# xenLae2.upstreamMaf = multiz9way /hive/data/genomes/xenTro7/bed/multiz9way/species.list

# xenTro10 'Xenopus tropicalis' GCF_000004195.4_UCB_Xtro_10.0
xenTro10.serverGenome = /hive/data/genomes/xenTro10/xenTro10.2bit
xenTro10.ooc = /hive/data/genomes/xenTro10/jkStuff/xenTro10.11.ooc
xenTro10.lift = /hive/data/genomes/xenTro10/jkStuff/xenTro10.gaps.lft
xenTro10.perChromTables = no
xenTro10.downloadDir = xenTro10
# xenTro10.mgc = yes
xenTro10.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
xenTro10.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
xenTro10.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
xenTro10.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
xenTro10.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# xenTro10.upstreamGeneTbl = ensGene
# xenTro10.upstreamMaf = multiz9way /hive/data/genomes/xenTro7/bed/multiz9way/species.list

# xenTro9 'Xenopus tropicalis' 11 chroms + 6811 contigs
xenTro9.serverGenome = /hive/data/genomes/xenTro9/xenTro9.2bit
xenTro9.ooc = /hive/data/genomes/xenTro9/jkStuff/xenTro9.11.ooc
xenTro9.lift = no
xenTro9.perChromTables = no
xenTro9.downloadDir = xenTro9
# xenTro9.mgc = yes
xenTro9.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
xenTro9.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
xenTro9.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
xenTro9.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
xenTro9.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# xenTro9.upstreamGeneTbl = ensGene
# xenTro9.upstreamMaf = multiz9way /hive/data/genomes/xenTro7/bed/multiz9way/species.list

# xenTro7 'Xenopus tropicalis' 7728 scaffolds
xenTro7.serverGenome = /hive/data/genomes/xenTro7/xenTro7.2bit
xenTro7.ooc = /hive/data/genomes/xenTro7/jkStuff/xenTro7.11.ooc
xenTro7.lift = no
xenTro7.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
xenTro7.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
xenTro7.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
xenTro7.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
xenTro7.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
xenTro7.refseq.mrna.native.load = yes
xenTro7.genbank.est.native.load = yes
xenTro7.refseq.mrna.xeno.load = yes
xenTro7.refseq.mrna.xeno.loadDesc = yes
xenTro7.genbank.mrna.xeno.load = no
xenTro7.downloadDir = xenTro7
xenTro7.perChromTables = no
xenTro7.mgc = yes
# xenTro7.upstreamGeneTbl = ensGene
# xenTro7.upstreamMaf = multiz9way /hive/data/genomes/xenTro7/bed/multiz9way/species.list


# xenTro3 (X. tropicalis) 19550 scaffolds
xenTro3.serverGenome = /hive/data/genomes/xenTro3/xenTro3.2bit
xenTro3.ooc = /hive/data/genomes/xenTro3/xenTro3.11.ooc
xenTro3.lift = no
xenTro3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
xenTro3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
xenTro3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
xenTro3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
xenTro3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
xenTro3.refseq.mrna.native.load = yes
xenTro3.genbank.est.native.load = yes
xenTro3.refseq.mrna.xeno.load = no
xenTro3.genbank.mrna.xeno.load = no
xenTro3.downloadDir = xenTro3
xenTro3.perChromTables = no
xenTro3.mgc = yes
xenTro3.upstreamGeneTbl = ensGene
xenTro3.upstreamMaf = multiz9way /hive/data/genomes/xenTro3/bed/multiz9way/species.list

# xenTro2 (X. tropicalis) 19579 scaffolds
xenTro2.serverGenome = /hive/data/genomes/xenTro2/xenTro2.2bit
xenTro2.ooc = /hive/data/genomes/xenTro2/11.ooc
xenTro2.lift = no
xenTro2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
xenTro2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
xenTro2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
xenTro2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
xenTro2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
xenTro2.refseq.mrna.native.load = yes
xenTro2.genbank.mrna.xeno.load = no
xenTro2.downloadDir = xenTro2
xenTro2.perChromTables = no
xenTro2.mgc = yes
xenTro2.upstreamGeneTbl = mgcGenes
xenTro2.upstreamMaf = multiz7way /hive/data/genomes/xenTro2/bed/multiz7way/species.lst

# xenTro1 (X. tropicalis) 27064 scaffolds!
xenTro1.serverGenome = /hive/data/genomes/xenTro1/xenTro1.2bit
xenTro1.ooc = /hive/data/genomes/xenTro1/11.ooc
xenTro1.lift = no
xenTro1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
xenTro1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
xenTro1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
xenTro1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
xenTro1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
xenTro1.refseq.mrna.native.load = no
xenTro1.genbank.mrna.xeno.load = no
xenTro1.downloadDir = xenTro1
xenTro1.perChromTables = no
xenTro1.mgc = yes
xenTro1.upstreamGeneTbl = mgcGenes
xenTro1.upstreamMaf = multiz5way /hive/data/genomes/xenTro1/bed/multiz/species.lst

# anoCar2 (A. carolinensis)
anoCar2.serverGenome = /hive/data/genomes/anoCar2/anoCar2.2bit
anoCar2.ooc = /hive/data/genomes/anoCar2/anoCar2.11.ooc
anoCar2.lift = /hive/data/genomes/anoCar2/nonBridged.lift
anoCar2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
anoCar2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
anoCar2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
anoCar2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
anoCar2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
anoCar2.refseq.mrna.native.load = no
anoCar2.genbank.est.native.load = yes
anoCar2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
anoCar2.genbank.mrna.xeno.load = yes
anoCar2.downloadDir = anoCar2
anoCar2.perChromTables = no
anoCar2.upstreamGeneTbl = ensGene
anoCar2.upstreamMaf = multiz7way /hive/data/genomes/anoCar2/bed/multiz7way/species.list

# anoCar1 (A. carolinensis)
anoCar1.serverGenome = /hive/data/genomes/anoCar1/anoCar1.2bit
anoCar1.ooc = /hive/data/genomes/anoCar1/11.ooc
anoCar1.lift = no
anoCar1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
anoCar1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
anoCar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
anoCar1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
anoCar1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
anoCar1.refseq.mrna.native.load = no
anoCar1.genbank.est.native.load = no
anoCar1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
anoCar1.downloadDir = anoCar1
anoCar1.perChromTables = no
anoCar1.upstreamGeneTbl = ensGene

# thaSir1 (Thamnophis sirtalis/Garter snake taxId 35019 GCF_001077635.1)
#          7930 contigs
thaSir1.serverGenome = /hive/data/genomes/thaSir1/thaSir1.2bit
thaSir1.ooc = /hive/data/genomes/thaSir1/jkStuff/thaSir1.11.ooc
thaSir1.lift = no
thaSir1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
thaSir1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
thaSir1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
thaSir1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
thaSir1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
thaSir1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
# defaults yes: genbank.mrna.native.load genbank.mrna.native.loadDesc
# yes: genbank.est.native.load refseq.mrna.native.load
# yes: refseq.mrna.native.loadDesc refseq.mrna.xeno.load
# yes: refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load genbank.mrna.xeno.loadDesc
# no: genbank.est.native.loadDesc genbank.est.xeno.load
# no: genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse
thaSir1.downloadDir = thaSir1
thaSir1.perChromTables = no
# thaSir1.upstreamGeneTbl = ensGene

# macEug1  (wallaby)
macEug1.serverGenome = /hive/data/genomes/macEug1/macEug1.2bit
macEug1.ooc = /hive/data/genomes/macEug1/macEug1.11.ooc
macEug1.lift = no
macEug1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
macEug1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
macEug1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
macEug1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
macEug1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
macEug1.refseq.mrna.native.load = no
macEug1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
macEug1.genbank.est.native.load = no
macEug1.downloadDir = macEug1
macEug1.perChromTables = no
macEug1.upstreamGeneTbl = xenoRefGene

# macEug2 (wallaby)
macEug2.serverGenome = /hive/data/genomes/macEug2/macEug2.2bit
macEug2.ooc = /hive/data/genomes/macEug2/macEug2.11.ooc
macEug2.lift = no
macEug2.perChromTables = no
macEug2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
macEug2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
macEug2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
macEug2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
macEug2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
macEug2.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
macEug2.downloadDir = macEug2
macEug2.refseq.mrna.native.load  = no
macEug2.refseq.mrna.xeno.load = yes
macEug2.refseq.mrna.xeno.loadDesc  = yes
macEug2.genbank.est.native.load = yes
macEug2.genbank.est.native.loadDesc = yes
macEug2.genbank.mrna.native.load = yes
macEug2.genbank.mrna.native.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
macEug2.genbank.est.native.load = yes
macEug2.genbank.est.native.loadDesc = yes

# triMan1  (manatee)
triMan1.serverGenome = /hive/data/genomes/triMan1/triMan1.2bit
triMan1.ooc = /hive/data/genomes/triMan1/jkStuff/triMan1.11.ooc
triMan1.lift = no
triMan1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
triMan1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
triMan1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
triMan1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
triMan1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
triMan1.refseq.mrna.native.load = no
triMan1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
triMan1.genbank.est.native.load = no
triMan1.downloadDir = triMan1
triMan1.perChromTables = no

# dasNov1  (armadillo)
dasNov1.serverGenome = /hive/data/genomes/dasNov1/dasNov1.2bit
dasNov1.ooc = /hive/data/genomes/dasNov1/11.ooc
dasNov1.lift = no
dasNov1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
dasNov1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
dasNov1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
dasNov1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
dasNov1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
dasNov1.refseq.mrna.native.load = no
dasNov1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
dasNov1.genbank.est.native.load = no
dasNov1.downloadDir = dasNov1
dasNov1.perChromTables = no

# loxAfr3 (elephant)
loxAfr3.serverGenome = /hive/data/genomes/loxAfr3/loxAfr3.2bit
loxAfr3.ooc = /hive/data/genomes/loxAfr3/loxAfr3.11.ooc
loxAfr3.lift = no
loxAfr3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
loxAfr3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
loxAfr3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
loxAfr3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
loxAfr3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
loxAfr3.refseq.mrna.native.load = yes
loxAfr3.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
loxAfr3.genbank.mrna.xeno.load = yes
loxAfr3.genbank.est.native.load = no
loxAfr3.downloadDir = loxAfr3
loxAfr3.perChromTables = no
loxAfr3.upstreamGeneTbl = ensGene

# loxAfr1 (elephant)
loxAfr1.serverGenome = /hive/data/genomes/loxAfr1/loxAfr1.2bit
loxAfr1.ooc = /hive/data/genomes/loxAfr1/11.ooc
loxAfr1.lift = no
loxAfr1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
loxAfr1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
loxAfr1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
loxAfr1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
loxAfr1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
loxAfr1.refseq.mrna.native.load = no
loxAfr1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
loxAfr1.genbank.est.native.load = no
loxAfr1.downloadDir = loxAfr1
loxAfr1.perChromTables = no

# echTel2 (tenrec)
echTel2.serverGenome = /hive/data/genomes/echTel2/echTel2.2bit
echTel2.ooc = /hive/data/genomes/echTel2/jkStuff/echTel2.11.ooc
echTel2.lift = no
echTel2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
echTel2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
echTel2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
echTel2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
echTel2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
echTel2.refseq.mrna.native.load = no
echTel2.refseq.mrna.xeno.load = yes
echTel2.genbank.mrna.xeno.load = no
echTel2.genbank.est.native.load = no
echTel2.genbank.mrna.native.load = no
echTel2.genbank.mrna.native.loadDesc = no
echTel2.downloadDir = echTel2
echTel2.perChromTables = no

# echTel1 (tenrec)
echTel1.serverGenome = /hive/data/genomes/echTel1/echTel1.2bit
echTel1.ooc = /hive/data/genomes/echTel1/jkStuff/echTel1.11.ooc
echTel1.lift = no
echTel1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
echTel1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
echTel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
echTel1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
echTel1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
echTel1.refseq.mrna.native.load = no
echTel1.refseq.mrna.xeno.load = yes
echTel1.genbank.mrna.xeno.load = no
echTel1.genbank.est.native.load = no
echTel1.genbank.mrna.native.load = no
echTel1.genbank.mrna.native.loadDesc = no
echTel1.downloadDir = echTel1
echTel1.perChromTables = no

# oryCun2 (rabbit)
oryCun2.serverGenome = /hive/data/genomes/oryCun2/oryCun2.2bit
oryCun2.ooc = /hive/data/genomes/oryCun2/oryCun2.11.ooc
oryCun2.lift = /hive/data/genomes/oryCun2/oryCun2.contigs.lift
oryCun2.perChromTables = no
oryCun2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
oryCun2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
oryCun2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
oryCun2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
oryCun2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
oryCun2.genbank.est.xeno.pslCDnaFilter    = ${ordered.genbank.est.xeno.pslCDnaFilter}
oryCun2.downloadDir = oryCun2
oryCun2.refseq.mrna.native.load  = yes
oryCun2.refseq.mrna.xeno.load = yes
oryCun2.refseq.mrna.xeno.loadDesc  = yes
oryCun2.genbank.mrna.xeno.load  = yes
oryCun2.upstreamGeneTbl = xenoRefGene

# oryCun1 (rabbit)
oryCun1.serverGenome = /hive/data/genomes/oryCun1/oryCun1.2bit
oryCun1.ooc = no
oryCun1.lift = no
oryCun1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
oryCun1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
oryCun1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
oryCun1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
oryCun1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
oryCun1.refseq.mrna.native.load = no
oryCun1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
oryCun1.genbank.est.native.load = yes
oryCun1.downloadDir = oryCun1
oryCun1.perChromTables = no

# cavApe1 Cavia aperea (Brazilian guinea pig) taxId: 37548
cavApe1.serverGenome = /hive/data/genomes/cavApe1/cavApe1.2bit
cavApe1.ooc = /hive/data/genomes/cavApe1/jkStuff/cavApe1.11.ooc
cavApe1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
cavApe1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
cavApe1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
cavApe1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
cavApe1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
cavApe1.lift = /hive/data/genomes/cavApe1/jkStuff/nonBridged.lft
cavApe1.downloadDir = cavApe1
cavApe1.perChromTables = no
# there are no native anything
cavApe1.refseq.mrna.native.load = no
cavApe1.refseq.mrna.native.loadDesc = no
cavApe1.genbank.mrna.native.load = no
cavApe1.genbank.mrna.native.loadDesc = no
# defaults yes: genbank.mrna.native.load and loadDesc
# defaults yes: genbank.est.native.load
# defaults yes: refseq.mrna.native.load, refseq.mrna.native.loadDesc
# defaults yes: refseq.mrna.xeno.load, refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load and loadDesc
# defaults no: genbank.est.xeno.load, genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse

# cavPor3 (C. porcellus) 3144 scaffolds 967 are multi-contig and 2076 are single contig
cavPor3.serverGenome = /hive/data/genomes/cavPor3/cavPor3.2bit
cavPor3.ooc = /hive/data/genomes/cavPor3/cavPor3.11.ooc
cavPor3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
cavPor3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
cavPor3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
cavPor3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
cavPor3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
cavPor3.lift = no
cavPor3.downloadDir = cavPor3
cavPor3.perChromTables = no
cavPor3.refseq.mrna.native.load = yes
cavPor3.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
cavPor3.genbank.mrna.xeno.load = yes
cavPor3.genbank.est.native.load = yes
cavPor3.upstreamGeneTbl = xenoRefGene
cavPor3.upstreamMaf = multiz8way /hive/data/genomes/cavPor3/bed/multiz8way/species.list

# ornAna2 (Platypus -- Ornithorhynchus anatinus)
ornAna2.serverGenome = /hive/data/genomes/ornAna2/ornAna2.2bit
ornAna2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ornAna2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ornAna2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ornAna2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ornAna2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
ornAna2.ooc = /hive/data/genomes/ornAna2/jkStuff/ornAna2.11.ooc
ornAna2.lift = no
ornAna2.refseq.mrna.xeno.load  = yes
ornAna2.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
ornAna2.genbank.mrna.xeno.load = no
ornAna2.downloadDir = ornAna2
ornAna2.perChromTables = no
# ornAna2.upstreamGeneTbl = ensGene
# ornAna2.upstreamMaf = multiz6way /hive/data/genomes/ornAna1/bed/multiz6way.2007-04-24/species.lst

# ornAna1 (Platypus -- O. anatinus)
ornAna1.serverGenome = /hive/data/genomes/ornAna1/ornAna1.2bit
ornAna1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
ornAna1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
ornAna1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
ornAna1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
ornAna1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
ornAna1.ooc = /hive/data/genomes/ornAna1/11.ooc
ornAna1.lift = no
ornAna1.refseq.mrna.xeno.load  = yes
ornAna1.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
ornAna1.genbank.mrna.xeno.load = yes
ornAna1.downloadDir = ornAna1
ornAna1.perChromTables = no
ornAna1.upstreamGeneTbl = ensGene
ornAna1.upstreamMaf = multiz6way /hive/data/genomes/ornAna1/bed/multiz6way.2007-04-24/species.lst

# petMar3 (Petromyzon marinus - Sea Lamprey - taxId 7757)
petMar3.serverGenome = /hive/data/genomes/petMar3/petMar3.2bit
petMar3.ooc = /hive/data/genomes/petMar3/jkStuff/petMar3.11.ooc
petMar3.lift = no
petMar3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
petMar3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
petMar3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
petMar3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
petMar3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
# defaults yes: genbank.mrna.native.load and loadDesc
# defaults yes: genbank.est.native.load
# defaults yes: refseq.mrna.native.load, refseq.mrna.native.loadDesc
# defaults yes: refseq.mrna.xeno.load, refseq.mrna.xeno.loadDesc
# defaults no: genbank.mrna.xeno.load and loadDesc
# defaults no: genbank.est.xeno.load, genbank.est.xeno.loadDesc
# DO NOT NEED genbank.mrna.xeno except for human, mouse
petMar3.downloadDir = petMar3
petMar3.perChromTables = no

# petMar2 (Petromyzon marinus - Sea Lamprey)
petMar2.serverGenome = /hive/data/genomes/petMar2/petMar2.2bit
petMar2.ooc = /hive/data/genomes/petMar2/jkStuff/petMar2.11.ooc
petMar2.lift = no
petMar2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
petMar2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
petMar2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
petMar2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
petMar2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
petMar2.refseq.mrna.native.load = yes
petMar2.refseq.mrna.xeno.load = yes
petMar2.genbank.mrna.xeno.load = no
petMar2.genbank.est.native.load = yes
petMar2.downloadDir = petMar2
petMar2.perChromTables = no
petMar2.upstreamGeneTbl = xenoRefGene
petMar2.upstreamMaf = multiz7way /hive/data/genomes/petMar2/bed/multiz7way/species.list

# petMar1 (Petromyzon marinus - Sea Lamprey)
petMar1.serverGenome = /hive/data/genomes/petMar1/petMar1.2bit
petMar1.ooc = /hive/data/genomes/petMar1/petMar1.11.ooc
petMar1.lift = no
petMar1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
petMar1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
petMar1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
petMar1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
petMar1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
petMar1.refseq.mrna.native.load = yes
petMar1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
petMar1.genbank.mrna.xeno.load = yes
petMar1.genbank.est.native.load = yes
petMar1.downloadDir = petMar1
petMar1.perChromTables = no
petMar1.upstreamGeneTbl = xenoRefGene
petMar1.upstreamMaf = multiz6way /hive/data/genomes/petMar1/bed/multiz6way/species.list

# braFlo2 (Branchiostoma floridae - Lancelet)
braFlo2.serverGenome = /hive/data/genomes/braFlo2/braFlo2.2bit
braFlo2.ooc = /hive/data/genomes/braFlo2/jkStuff/braFlo2.11.ooc
braFlo2.lift = /hive/data/genomes/braFlo2/jkStuff/braFlo2.nonBridged.lift
braFlo2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
braFlo2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
braFlo2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
braFlo2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
braFlo2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
braFlo2.refseq.mrna.native.load = yes
braFlo2.refseq.mrna.xeno.load = yes
braFlo2.genbank.mrna.xeno.load = no
braFlo2.genbank.est.native.load = yes
braFlo2.downloadDir = braFlo2
braFlo2.perChromTables = no

# braFlo1 (Branchiostoma floridae - Lancelet)
braFlo1.serverGenome = /hive/data/genomes/braFlo1/braFlo1.2bit
braFlo1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
braFlo1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
braFlo1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
braFlo1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
braFlo1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
braFlo1.ooc = /hive/data/genomes/braFlo1/11.ooc
braFlo1.lift = /hive/data/genomes/braFlo1/jkStuff/liftAll.lft
braFlo1.refseq.mrna.native.load = no
braFlo1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
braFlo1.genbank.mrna.xeno.load = yes
braFlo1.genbank.est.native.load = yes
braFlo1.downloadDir = braFlo1
braFlo1.perChromTables = no
braFlo1.upstreamGeneTbl = xenoRefGene
braFlo1.upstreamMaf = multiz5way /hive/data/genomes/braFlo1/bed/multiz5way/species.list

# oxyTri2 (Oxytricha trifallax)
oxyTri2.serverGenome = /hive/data/genomes/oxyTri2/oxyTri2.2bit
oxyTri2.ooc = /hive/data/genomes/oxyTri2/jkStuff/oxyTri2.11.ooc
oxyTri2.lift = /hive/data/genomes/oxyTri2/jkStuff/oxyTri2.nonBridged.lft
oxyTri2.perChromTables = no
oxyTri2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
oxyTri2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
oxyTri2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
oxyTri2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
oxyTri2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
oxyTri2.genbank.est.xeno.pslCDnaFilter    = ${finished.genbank.est.xeno.pslCDnaFilter}
oxyTri2.downloadDir = oxyTri2
# defaults are OK: genbank and refseq mrna.native.load yes
#                  genbank est.native.load yes refseq.mrna.xeno.load yes
#                  genbank mrna and est xeno.load no

# droAna1 (D. ananassae)
droAna1.serverGenome = /hive/data/genomes/droAna1/droAna1.2bit
droAna1.ooc = /hive/data/genomes/droAna1/11.ooc
droAna1.lift = no
droAna1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droAna1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droAna1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droAna1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droAna1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droAna1.refseq.mrna.native.load = no
droAna1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# GenBank has no D. ananassae ESTs at this point... that may change.
droAna1.genbank.est.native.load = no
droAna1.downloadDir = droAna1
droAna1.perChromTables = no

# droAna2 (D. ananassae)
droAna2.serverGenome = /hive/data/genomes/droAna2/droAna2.2bit
droAna2.ooc = /hive/data/genomes/droAna2/11.ooc
droAna2.lift = no
droAna2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droAna2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droAna2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droAna2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droAna2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droAna2.refseq.mrna.native.load = no
droAna2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# GenBank has no D. ananassae ESTs at this point... that may change.
droAna2.genbank.est.native.load = no
droAna2.downloadDir = droAna2
droAna2.perChromTables = no

# droMoj1 (D. mojavensis)
droMoj1.serverGenome = /hive/data/genomes/droMoj1/droMoj1.2bit
droMoj1.ooc = /hive/data/genomes/droMoj1/11.ooc
droMoj1.lift = no
droMoj1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droMoj1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droMoj1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droMoj1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droMoj1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droMoj1.refseq.mrna.native.load = no
droMoj1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# GenBank has no D. mojavensis ESTs at this point... that may change.
droMoj1.genbank.est.native.load = no
droMoj1.downloadDir = droMoj1
droMoj1.perChromTables = no

# droMoj2 (D. mojavensis)
# genbank has 1 mRNA and 0 ESTs at time of initial build
droMoj2.serverGenome = /hive/data/genomes/droMoj2/droMoj2.2bit
droMoj2.ooc = /hive/data/genomes/droMoj2/11.ooc
droMoj2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droMoj2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droMoj2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droMoj2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droMoj2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droMoj2.lift = no
droMoj2.refseq.mrna.native.load = no
droMoj2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
droMoj2.genbank.est.native.load = no
droMoj2.downloadDir = droMoj2
droMoj2.perChromTables = no

# droVir1 (D. virilis)
droVir1.serverGenome = /hive/data/genomes/droVir1/droVir1.2bit
droVir1.ooc = /hive/data/genomes/droVir1/11.ooc
droVir1.lift = no
droVir1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droVir1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droVir1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droVir1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droVir1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droVir1.refseq.mrna.native.load = no
droVir1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# GenBank has no D. virilis ESTs at this point... that may change.
droVir1.genbank.est.native.load = no
droVir1.downloadDir = droVir1
droVir1.perChromTables = no

# droVir2 (D. virilis)
# genbank has 35 mRNAs and 633 ESTs at time of initial build
droVir2.serverGenome = /hive/data/genomes/droVir2/droVir2.2bit
droVir2.ooc = /hive/data/genomes/droVir2/11.ooc
droVir2.lift = no
droVir2.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droVir2.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droVir2.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droVir2.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droVir2.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droVir2.refseq.mrna.native.load = yes
droVir2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
droVir2.genbank.est.native.load = yes
droVir2.downloadDir = droVir2
droVir2.perChromTables = no

# apiMel1 (A. mellifera)
apiMel1.serverGenome = /hive/data/genomes/apiMel1/apiMel1.2bit
apiMel1.ooc = /hive/data/genomes/apiMel2/11.ooc
apiMel1.lift = no
apiMel1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
apiMel1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
apiMel1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
apiMel1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
apiMel1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
apiMel1.refseq.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
apiMel1.downloadDir = apiMel1
apiMel1.perChromTables = no

# apiMel2 (A. mellifera)
apiMel2.serverGenome = /hive/data/genomes/apiMel2/nib/*.nib
apiMel2.ooc = /hive/data/genomes/apiMel2/11.ooc
apiMel2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
apiMel2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
apiMel2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
apiMel2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
apiMel2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
apiMel2.lift = no
apiMel2.refseq.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
apiMel2.genbank.mrna.xeno.load = yes
apiMel2.downloadDir = apiMel2
apiMel2.perChromTables = no

# droEre1 (D. erecta)
droEre1.serverGenome = /hive/data/genomes/droEre1/droEre1.2bit
droEre1.ooc = /hive/data/genomes/droEre1/11.ooc
droEre1.lift = no
droEre1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droEre1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droEre1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droEre1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droEre1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droEre1.refseq.mrna.native.load = no
droEre1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
droEre1.genbank.mrna.xeno.load = yes
# GenBank has no D. erecta ESTs at this point... that may change.
droEre1.genbank.est.native.load = no
droEre1.downloadDir = droEre1
droEre1.perChromTables = no

# monDom5 (M. domestica)  8 chroms plus X and Un
monDom5.serverGenome = /hive/data/genomes/monDom5/monDom5.2bit
monDom5.ooc = /hive/data/genomes/monDom5/11.ooc
monDom5.lift = /hive/data/genomes/monDom5/jkStuff/liftAll.lft
monDom5.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
monDom5.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
monDom5.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
monDom5.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
monDom5.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
monDom5.downloadDir = monDom5
monDom5.refseq.mrna.xeno.load  = yes
monDom5.refseq.mrna.xeno.loadDesc = yes
monDom5.genbank.mrna.xeno.load  = yes
monDom5.perChromTables = no
monDom5.upstreamGeneTbl = refGene
monDom5.upstreamMaf = multiz9way /hive/data/genomes/monDom5/bed/multiz9way/species.lst

# monDom4 (M. domestica)  8 chroms plus X and Un
monDom4.serverGenome = /hive/data/genomes/monDom4/monDom4.2bit
monDom4.ooc = /hive/data/genomes/monDom4/11.ooc
monDom4.lift = no
monDom4.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
monDom4.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
monDom4.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
monDom4.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
monDom4.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
monDom4.downloadDir = monDom4
monDom4.refseq.mrna.xeno.load  = yes
monDom4.refseq.mrna.xeno.loadDesc = yes
monDom4.upstreamGeneTbl = ensGene
monDom4.upstreamMaf = multiz7way /hive/data/genomes/monDom4/bed/multiz7way/species.lst

# monDom1 (M. domestica)  19,348 scaffolds
monDom1.serverGenome = /hive/data/genomes/monDom1/monDom1.2bit
monDom1.ooc = /hive/data/genomes/monDom1/11.ooc
monDom1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
monDom1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
monDom1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
monDom1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
monDom1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
monDom1.refseq.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
monDom1.genbank.est.native.load = no
monDom1.downloadDir = monDom1
monDom1.lift = no
monDom1.perChromTables = no
# there is no suitable gene table here
# monDom1.upstreamGeneTbl = ensGene

# cb3 (C. briggsae)
cb3.serverGenome = /hive/data/genomes/cb3/cb3.2bit
cb3.ooc = /hive/data/genomes/cb3/11.ooc
cb3.lift = /hive/data/genomes/cb3/jkStuff/liftAll.lft
cb3.align.unplacedChroms = chrUn,chr*_random
cb3.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
cb3.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
cb3.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
cb3.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
cb3.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
cb3.refseq.mrna.native.load = no
cb3.refseq.mrna.xeno.load  = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
cb3.genbank.mrna.xeno.load = yes
cb3.downloadDir = cb3

# cb1 (C. briggsae)
cb1.serverGenome = /hive/data/genomes/cb1/chrUn.2bit
cb1.ooc = /hive/data/genomes/cb1/11.ooc
cb1.align.unplacedChroms = chrUn
cb1.lift = /hive/data/genomes/cb1/Un/chrUn.lft
cb1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
cb1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
cb1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
cb1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
cb1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
cb1.refseq.mrna.native.load = yes
cb1.refseq.mrna.xeno.load = yes
cb1.genbank.mrna.xeno.load = no
cb1.downloadDir = cbJul2002
cb1.perChromTables = no

# droSim1 (D. simulans)
droSim1.serverGenome = /hive/data/genomes/droSim1/droSim1.2bit
droSim1.ooc = /hive/data/genomes/droSim1/11.ooc
droSim1.lift = /hive/data/genomes/droSim1/jkStuff/liftAll.lft
droSim1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droSim1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droSim1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droSim1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droSim1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droSim1.refseq.mrna.native.load = no
droSim1.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
droSim1.genbank.mrna.xeno.load = yes
droSim1.downloadDir = droSim1

# droGri1 (D. grimshawi)
droGri1.serverGenome = /hive/data/genomes/droGri1/droGri1.2bit
droGri1.lift = no
droGri1.ooc=/hive/data/genomes/droGri1/11.ooc
droGri1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droGri1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droGri1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droGri1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droGri1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droGri1.refseq.mrna.native.load = no
droGri1.refseq.mrna.xeno.load = yes
# GenBank has no D. grimshawi mRNAs nor ESTs at this point... that may change.
droGri1.genbank.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
droGri1.genbank.est.native.load = no
droGri1.downloadDir = droGri1
droGri1.perChromTables = no

# droYak2 (D. yakuba)
droYak2.serverGenome = /hive/data/genomes/droYak2/droYak2.2bit
droYak2.ooc = /hive/data/genomes/droYak2/11.ooc
droYak2.lift = /hive/data/genomes/droYak2/jkStuff/liftAll.lft
droYak2.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
droYak2.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
droYak2.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
droYak2.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
droYak2.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
droYak2.refseq.mrna.native.load = no
droYak2.refseq.mrna.xeno.load = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
droYak2.downloadDir = droYak2

# droPer1 (D. persimilis)
# genbank.150.0/full has 1 mRNA and 0 ESTs at time of initial build,
# so no need to make native tracks.
droPer1.serverGenome = /hive/data/genomes/droPer1/droPer1.2bit
droPer1.ooc = /hive/data/genomes/droPer1/11.ooc
droPer1.lift = no
droPer1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droPer1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droPer1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droPer1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droPer1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droPer1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
droPer1.refseq.mrna.native.load = no
droPer1.refseq.mrna.xeno.load = yes
droPer1.genbank.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
droPer1.genbank.est.native.load = no
droPer1.downloadDir = droPer1
droPer1.perChromTables = no

# droSec1 (D. sechellia)
# genbank.150.0/full has 7 mRNAs and 0 ESTs at time of initial build,
# so no need to make native tracks.
droSec1.serverGenome = /hive/data/genomes/droSec1/droSec1.2bit
droSec1.ooc = /hive/data/genomes/droSec1/11.ooc
droSec1.lift = no
droSec1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
droSec1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
droSec1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
droSec1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
droSec1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
droSec1.genbank.est.xeno.pslCDnaFilter    = ${lowCover.genbank.est.xeno.pslCDnaFilter}
droSec1.refseq.mrna.native.load = no
droSec1.refseq.mrna.xeno.load = yes
droSec1.genbank.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
droSec1.genbank.mrna.xeno.load = yes
droSec1.genbank.est.native.load = no
droSec1.downloadDir = droSec1
droSec1.perChromTables = no

# nemVec1 (Starlet Sea Anemone)
# Per Mark: only load if >10^3 available - /hive/data/genomes/genbank/data/organism.lst
# organism                mrnaCnt    estCnt  refSeqCnt
nemVec1.serverGenome = /hive/data/genomes/nemVec1/nemVec1.2bit
nemVec1.ooc = /hive/data/genomes/nemVec1/11.ooc
nemVec1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
nemVec1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
nemVec1.genbank.est.native.pslCDnaFilter  = ${lowCover.genbank.est.native.pslCDnaFilter}
nemVec1.maxIntron = 100000
nemVec1.lift = no
nemVec1.genbank.est.native.load = yes
nemVec1.genbank.est.xeno.load = no
nemVec1.genbank.mrna.native.load = no
# DO NOT NEED genbank.mrna.xeno except for human, mouse
nemVec1.refseq.mrna.xeno.load = yes
nemVec1.refseq.mrna.native.load = no
nemVec1.perChromTables = no
nemVec1.downloadDir = nemVec1

# aplCal1 - (Sea Hare Broad WGS Aplcal 2.0)
#       Assembly Accession: AASC00000000.2
aplCal1.serverGenome = /hive/data/genomes/aplCal1/aplCal1.2bit
aplCal1.ooc = /hive/data/genomes/aplCal1/11.ooc
aplCal1.refseq.mrna.native.pslCDnaFilter  = ${lowCover.refseq.mrna.native.pslCDnaFilter}
aplCal1.refseq.mrna.xeno.pslCDnaFilter    = ${lowCover.refseq.mrna.xeno.pslCDnaFilter}
aplCal1.genbank.mrna.native.pslCDnaFilter = ${lowCover.genbank.mrna.native.pslCDnaFilter}
aplCal1.genbank.mrna.xeno.pslCDnaFilter   = ${lowCover.genbank.mrna.xeno.pslCDnaFilter}
aplCal1.genbank.est.native.pslCDnaFilter = ${lowCover.genbank.est.native.pslCDnaFilter}
aplCal1.genbank.est.xeno.pslCDnaFilter   = ${lowCover.genbank.est.xeno.pslCDnaFilter}
aplCal1.refseq.mrna.native.load  = no
aplCal1.genbank.est.native.load = yes
aplCal1.genbank.est.xeno.load = no
aplCal1.refseq.mrna.xeno.load  = yes
aplCal1.refseq.mrna.xeno.loadDesc = yes
aplCal1.perChromTables = no
aplCal1.downloadDir = aplCal1
aplCal1.genbank.mrna.blatTargetDb = yes
aplCal1.lift = no

# staAur2 (Staphylococcus aureus -  Taxid: 93061)
staAur2.serverGenome = /hive/data/genomes/staAur2/staAur2.2bit
staAur2.ooc = /hive/data/genomes/staAur2/jkStuff/staAur2.11.ooc
staAur2.lift = no
staAur2.downloadDir = staAur2
staAur2.perChromTables = no
staAur2.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
staAur2.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
staAur2.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
staAur2.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
staAur2.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# staAur2.upstreamGeneTbl = ensGene
# staAur2.upstreamMaf = multiz9way /hive/data/genomes/staAur2/bed/multiz9way/species.list

# staAur1 (Staphylococcus aureus -  Taxid: 93061)
staAur1.serverGenome = /hive/data/genomes/staAur1/staAur1.2bit
staAur1.ooc = /hive/data/genomes/staAur1/jkStuff/staAur1.11.ooc
staAur1.lift = no
staAur1.downloadDir = staAur1
staAur1.perChromTables = no
staAur1.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
staAur1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
staAur1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
staAur1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
staAur1.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# staAur1.upstreamGeneTbl = ensGene
# staAur1.upstreamMaf = multiz9way /hive/data/genomes/staAur1/bed/multiz9way/species.list


# hbv1 (Hepatitis B virus - Taxid: 10407)
hbv1.serverGenome = /hive/data/genomes/hbv1/hbv1.2bit
hbv1.ooc = /hive/data/genomes/hbv1/jkStuff/hbv1.11.ooc
hbv1.lift = no
hbv1.downloadDir = hbv1
hbv1.perChromTables = no
hbv1.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
hbv1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
hbv1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
hbv1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
hbv1.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# trying mrna.xeno to see what loads
hbv1.genbank.mrna.xeno.load = yes
hbv1.genbank.mrna.xeno.loadDesc = yes
hbv1.refseq.mrna.xeno.load  = yes
hbv1.refseq.mrna.xeno.loadDesc = yes
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# hbv1.upstreamGeneTbl = ensGene
# hbv1.upstreamMaf = multiz9way /hive/data/genomes/hbv1/bed/multiz9way/species.list

# hpv1 (Human papillomavirus type 90 -  Taxid: 333769)
hpv1.serverGenome = /hive/data/genomes/hpv1/hpv1.2bit
hpv1.ooc = /hive/data/genomes/hpv1/jkStuff/hpv1.11.ooc
hpv1.lift = no
hpv1.downloadDir = hpv1
hpv1.perChromTables = no
hpv1.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
hpv1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
hpv1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
hpv1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
hpv1.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
# DO NOT NEED genbank.mrna.xeno except for human, mouse
# defaults yes: genbank.mrna.native.load, genbank.mrna.native.loadDesc,
# genbank.est.native.load, refseq.mrna.native.load, refseq.mrna.native.loadDesc,
# refseq.mrna.xeno.load , refseq.mrna.xeno.loadDesc
# hpv1.upstreamGeneTbl = ensGene
# hpv1.upstreamMaf = multiz9way /hive/data/genomes/hpv1/bed/multiz9way/species.list

# wuhCor1 (Severse acute respiratory syndrome coronavirus 2 -  Taxid: 2697049)
wuhCor1.serverGenome = /hive/data/genomes/wuhCor1/wuhCor1.2bit
wuhCor1.ooc = /hive/data/genomes/wuhCor1/jkStuff/wuhCor1.11.ooc
wuhCor1.lift = no
wuhCor1.downloadDir = wuhCor1
wuhCor1.perChromTables = no
wuhCor1.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
wuhCor1.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
wuhCor1.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
wuhCor1.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
wuhCor1.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}

#
# Please keep organisms together and in assending order rather than adding at
# the end
#
