# for emacs: -*- mode: sh; -*-

# This file describes browser build for the micOch1

# this browser started a long time ago as a manual one time shot,
#  this is a catch up procedure to fill in the standard details

#########################################################################
#  Initial steps, find photograph (DONE - 2017-01-25 - Hiram)

# To start this initialBuild.txt document, from a previous assembly document:

mkdir ~/kent/src/hg/makeDb/doc/micOch1
cd ~/kent/src/hg/makeDb/doc/micOch1

sed -e 's/galGal/melGal/g; s/GalGal/MelGal/g; s/TBD/TBD/g;' \
       ../galGal5/initialBuild.txt > initialBuild.txt

# there is now a refseq release since this was first built, it
# has not changed sequence.  Fetch for reference here:
mkdir /hive/data/genomes/micOch1/refseq
cd /hive/data/genomes/micOch1/refseq

rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Microtus_ochrogaster/all_assembly_versions/GCF_000317375.1_MicOch1.0/ ./

# sent 3299 bytes  received 2922069976 bytes  20221960.38 bytes/sec
# total size is 2921701078  speedup is 1.00
# real    2m23.342s

mkdir /hive/data/genomes/micOch1/photo
cd /hive/data/genomes/micOch1/photo
wget --timestamping \
http://wildlife.ohiodnr.gov/portals/wildlife/Species%20and%20Habitats/Species%20Guide%20Index/Images/prarievole.jpg
# the size is OK already and it is good quality

# construct the required photoReference.txt
cd /hive/data/genomes/micOch1
printf "photoCreditURL\t%s\nphotoCreditName\t%s\n" \
'http://wildlife.ohiodnr.gov/species-and-habitats/species-guide-index/mammals/prairie-vole' \
'Photo courtesy of the National Park Service' > photoReference.txt

# this information is from the top of 
#    micOch1/refseq/*_assembly_report.txt
#    ( aka: micOch1/refseq/GCF_000317375.1_MicOch1.0_assembly_report.txt )

# Assembly name:  MicOch1.0
# Organism name:  Microtus ochrogaster (prairie vole)
# Isolate:  Prairie Vole_2
# Sex:  female
# Taxid:          79684
# BioSample:      SAMN00727831
# BioProject:     PRJNA210839
# Submitter:      Broad Institute
# Date:           2012-12-7
# Assembly type:  haploid
# Release type:   major
# Assembly level: Chromosome
# Genome representation: full
# WGS project:    AHZW01
# Assembly method: allpaths v. R41985 HAPLOIDIFY=True SPRS_WRITE_SEPS=True
# Genome coverage: 94x
# Sequencing technology: Illumina Hi-Seq
# RefSeq category: Representative Genome
# GenBank assembly accession: GCA_000317375.1
# RefSeq assembly accession: GCF_000317375.1
# RefSeq assembly and GenBank assemblies identical: yes
#
## Assembly-Units:
## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
## GCA_000317385.1      GCF_000317385.1 Primary Assembly

#############################################################################
# establish config.ra file (DONE - Hiram - 2017-01-25)
    cd /hive/data/genomes/micOch1
    $HOME/kent/src/hg/utils/automation/prepConfig.pl \
micOch1 mammal micOch \
/hive/data/outside/ncbi/genomes/genbank/vertebrate_mammalian/Microtus_ochrogaster/all_assembly_versions/GCA_000317375.1_MicOch1.0/GCA_000317375.1_MicOch1.0_assembly_report.txt
       ./refseq/*_assembly_report.txt > micOch1.config.ra

    # verify it looks sane
    cat micOch1.config.ra
# config parameters for makeGenomeDb.pl:
db micOch1
clade mammal
scientificName Microtus ochrogaster
commonName Prairie vole
assemblyDate Dec. 2012
assemblyLabel Broad Institute
assemblyShortLabel MicOch1.0
orderKey 16759
mitoAcc none
fastaFiles /hive/data/genomes/micOch1/ucsc/*.fa
agpFiles /hive/data/genomes/micOch1/ucsc/*.agp
# qualFiles none
dbDbSpeciesDir micOch
photoCreditURL  http://wildlife.ohiodnr.gov/species-and-habitats/species-guide-index/mammals/prairie-vole
photoCreditName Photo courtesy of the National Park Service
ncbiGenomeId 10848
ncbiAssemblyId 504458
ncbiAssemblyName MicOch1.0
ncbiBioProject 210839
ncbiBioSample SAMN00727831
genBankAccessionID GCF_000317375.1
taxId 79684

    # and compare with how well it matches the existing dbDb entry:
    hgsql -e 'select * from dbDb where name="micOch1"\G' hgcentraltest

*************************** 1. row ***************************
          name: micOch1
   description: Oct 2012 (MicOch1.0/micOch1)
       nibPath: /gbdb/micOch1
      organism: Prairie vole
    defaultPos: chr1:50669050-76003576
        active: 1
      orderKey: 16760
        genome: Prairie vole
scientificName: Microtus ochrogaster
      htmlPath: /gbdb/micOch1/html/description.html
      hgNearOk: 0
        hgPbOk: 0
    sourceName: Broad Institute GCA_000317375.1
         taxId: 79684

     # that is close enough, only the date Oct. vs Dec. is different
     # It was Oct. in the genbank release in 2012
     # It does need the .
     hgsql -e 'update dbDb set description="Oct. 2012 (MicOch1.0/micOch1)" where name="micOch1";' hgcentraltest

#############################################################################
# setup UCSC named files (DONE - 2016-06-07 - Hiram)

    mkdir /hive/data/genomes/micOch1/ucsc
    cd /hive/data/genomes/micOch1/ucsc
    # measure what is in the refseq release:
    faSize ../refseq/GCF_000317375.1_MicOch1.0_genomic.fna.gz
# 2287340943 bases (183019268 N's 2104321675 real 1490270617 upper
#    614051058 lower) in 6335 sequences in 1 files
# Total size: mean 361064.1 sd 4482029.3 min 1000 (NW_004955401.1)
#    max 126672627 (NC_022009.1) median 2515
# %26.85 masked total, %29.18 masked real

    # compare to existing UCSC 2bit:
# 2287340943 bases (183019268 N's 2104321675 real 1601638277 upper
#    502683398 lower) in 6335 sequences in 1 files
# Total size: mean 361064.1 sd 4482029.3 min 1000 (chrUn_AHZW01186948)
#    max 126672627 (chr1) median 2515
# %21.98 masked total, %23.89 masked real

    # check for duplicate sequences:
    cd /hive/data/genomes/micOch1
    twoBitDup micOch1.2bit
    # no output is a good result, otherwise, would have to eliminate duplicates
    # the scripts creating the fasta here will be using this refseq.2bit file
    # remove it later

    # it appears the following scripts were used:
    $HOME/kent/src/hg/makeDb/doc/micOch1/unplaced.pl
    $HOME/kent/src/hg/makeDb/doc/micOch1/unlocalized.pl
    $HOME/kent/src/hg/makeDb/doc/micOch1/ucscCompositeAgp.pl

    # there was no chrM sequence in 2012.  There may be now, but it
    # can't be put into this sequence now

    # verify fasta and AGPs agree
    cd /hive/data/genomes/micOch1
    checkAgpAndFa micOch1.agp micOch1.2bit 2>&1 | tail -1
    #  All AGP and FASTA entries agree - both files are valid

#############################################################################
#  Initial database build (DONE - 2013-06-07 - Hiram)

    # one outstanding issues is the trackDb entry:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
      -fileServer=hgwdev -continue=trackDb micOch1.config.ra) > trackDb.log 2>&1
    # real    0m7.981s

    # check in the trackDb files created in TemporaryTrackDbCheckout/
    #    and add micOch1 to trackDb/makefile

    # temporary symlink until masked sequence is available
    cd /hive/data/genomes/micOch1
    ln -s `pwd`/micOch1.unmasked.2bit /gbdb/micOch1/micOch1.2bit

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2016-07-16 - Hiram)
    mkdir /hive/data/genomes/micOch1/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/micOch1/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/micOch1/micOch1.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku micOch1) > do.log 2>&1
    # real    24m14.786s

    cat fb.micOch1.cpgIslandExtUnmasked.txt
    # 11831917 bases of 2104321675 (0.562%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2017-01-25 - Hiram)
    mkdir /hive/data/genomes/micOch1/bed/cytoBand
    cd /hive/data/genomes/micOch1/bed/cytoBand
    makeCytoBandIdeo.csh micOch1

#########################################################################
# ucscToINSDC table/track (DONE - 2017-01-25 - Hiram)
    # this one is a bit different due to the older style UCSC names
    #  without the v1 version, and was then using genbank names

    mkdir /hive/data/genomes/micOch1/bed/ucscToINSDC
    cd /hive/data/genomes/micOch1/bed/ucscToINSDC


    grep -v "^#" \
      ../../genbank/Primary_Assembly/assembled_chromosomes/chr2acc \
          | awk '{printf "chr%s\t%s\n", $1, $2}' > t.txt

    grep -v "^#" \
    ../../genbank/Primary_Assembly/unlocalized_scaffolds/unlocalized.chr2scaf \
      | awk '{printf "chr%d_%s_random\t%s\n", $1, $2, $2}' \
         | sed -e 's/\.1//;' >> t.txt

    zcat ../../genbank/Primary_Assembly/unplaced_scaffolds/AGP/*.gz \
       | grep -v "^#" | awk '$5 != "N"'  | egrep "^JH|^AHZ" | cut -f1 \
          | sort -u | awk '{printf "%s\t%s\n", $1, $1}' \
             | sed -e 's/^/chrUn_/; s/\.1//;' >> t.txt

    sort -k2 t.txt > ucscToINSDC.txt
    rm -f t.txt

    awk '{printf "%s\t%s\n", $2, $1}' ucscToINSDC.txt | sort > insdcToUcsc.txt

    # extract the refseq vs. genbank names from the assembly_report
    grep -v "^#" ../../refseq/GCF*_assembly_report.txt | cut -f5,7 \
      | awk '{printf "%s\t%s\n", $2, $1}'  | sort -k2 > refseq.insdc.txt

    awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \
         | sort > name.coordinate.tab
    join -1 2 -2 2 refseq.insdc.txt ucscToINSDC.txt | tr '[ ]' '[\t]' \
       | sort -k3 \
       | join -2 3 name.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-3,4 \
           > ucscToINSDC.bed

    # should be same line counts throughout:
    wc -l *
    #	6335 insdcToUcsc.txt
    #	6335 name.coordinate.tab
    #	6335 refseq.insdc.txt
    #	6335 ucscToINSDC.bed
    #	6335 ucscToINSDC.txt

    cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1
    # 21
    # use the 21 in this sed
    sed -e "s/21/21/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
         | hgLoadSqlTab micOch1 ucscToINSDC stdin ucscToINSDC.bed
    checkTableCoords micOch1
    # should cover %100 entirely:
    featureBits -countGaps micOch1 ucscToINSDC
    # 2287340943 bases of 2287340943 (100.000%) in intersection

#########################################################################
# UCSC to RefSeq name correspondence (DONE - 2017-01-25 - Hiram)

    mkdir /hive/data/genomes/micOch1/bed/ucscToRefSeq
    cd /hive/data/genomes/micOch1/bed/ucscToRefSeq

    # the work for this is already done from above, just a different
    # column select on the final result:

    join -1 2 -2 2 ../ucscToINSDC/refseq.insdc.txt \
        ../ucscToINSDC/ucscToINSDC.txt | tr '[ ]' '[\t]' \
       | sort -k3 \
       | join -2 3 ../ucscToINSDC/name.coordinate.tab - \
           | tr '[ ]' '[\t]' | cut -f1-3,5 | sort -k1,1 -k2,2n > ucsc.refSeq.tab


    # verify same row count as above
    wc -l *.tab
    #	6335 ucsc.refSeq.tab

    export chrSize=`cut -f1 ucsc.refSeq.tab | awk '{print length($0)}' | sort -n | tail -1`
    echo $chrSize
    #  21
    sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
       | sed -e 's/INSDC/RefSeq/g;' > ucscToRefSeq.sql
    hgLoadSqlTab micOch1 ucscToRefSeq ./ucscToRefSeq.sql ucsc.refSeq.tab

    checkTableCoords  micOch1 -table=ucscToRefSeq
    # should cover %100 all bases:
    featureBits -countGaps micOch1 ucscToRefSeq
    # 2287340943 bases of 2287340943 (100.000%) in intersection

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2017-01-25 - Hiram)
    cd ~/kent/src/hg/makeDb/trackDb/micOch/micOch1
    # preview prefixes and suffixes:
    hgsql -N -e "select frag from gold;" micOch1 \
      | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c 
#   187012 AHZW.1

    # implies a rule: 'AHZW[0-9]+(\.[0-9]+)?'

    # verify this rule will find them all and eliminate them all:
    hgsql -N -e "select frag from gold;" micOch1 | wc -l
    # 187012

    hgsql -N -e "select frag from gold;" micOch1 \
       | egrep -e 'AHZW[0-9]+(\.[0-9]+)?' | wc -l
    # 187012

    hgsql -N -e "select frag from gold;" micOch1 \
       | egrep -v -e 'AHZW[0-9]+(\.[0-9]+)?' | wc -l
    # 0

    # hence, add to trackDb/micOch/micOch1/trackDb.ra
searchTable gold
shortCircuit 1
termRegex AHZW[0-9]+(\.[0-9]+)?
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 8

    # verify searches work in the position box

##########################################################################
# running repeat masker (DONE - 2013-06-12 - Hiram)
    mkdir /hive/data/genomes/micOch1/bed/repeatMasker
    cd /hive/data/genomes/micOch1/bed/repeatMasker
    time  (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku micOch1) > do.log 2>&1
    # real    579m2.068s

    cat faSize.rmsk.txt
# 2287340943 bases (183019268 N's 2104321675 real 1603144124 upper
#	501177551 lower) in 6335 sequences in 1 files
# Total size: mean 361064.1 sd 4482029.3 min 1000 (chrUn_AHZW01186948)
#	max 126672627 (chr1) median 2515
# %21.91 masked total, %23.82 masked real

    egrep -i "versi|relea" do.log
    # RepeatMasker version open-4.0.2
    # April 29 2013 (open-4-0-2) version of RepeatMasker
    # CC   RELEASE 20130422;    

    time featureBits -countGaps micOch1 rmsk
    # 501206092 bases of 2287340943 (21.912%) in intersection
    #  real    0m34.548s

    # why is it different than the faSize above ?
    # because rmsk masks out some N's as well as bases, the faSize count above
    #   separates out the N's from the bases, it doesn't show lower case N's

    # faster way to get the same result:
    time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' micOch1 \
        | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total"
    # total 501206092.000000
    #  real    0m26.341s

    time  (doRepeatMasker.pl -buildDir=`pwd` -continue=install \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku micOch1) > install.log 2>&1
    # real    12m11.673s

##########################################################################
# running simple repeat (DONE - 2013-06-07 - Hiram)

    mkdir /hive/data/genomes/micOch1/bed/simpleRepeat
    cd /hive/data/genomes/micOch1/bed/simpleRepeat
    # using trf409 3 here guessing smaller genome (human == 6)
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        -trf409 3 micOch1) > do.log 2>&1
    # real    16m52.479s

    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        -debug -continue=load -trf409 3 micOch1) > load.log 2>&1

    cat fb.simpleRepeat
    # 48159368 bases of 2104321675 (2.289%) in intersection

    cd /hive/data/genomes/micOch1
    # using the Window Masker result:
    cd /hive/data/genomes/micOch1
    twoBitMask bed/windowMasker/micOch1.cleanWMSdust.2bit \
       -add bed/simpleRepeat/trfMask.bed  micOch1.2bit
    #   you can safely ignore the warning about fields >= 13

    # add to rmsk after it is done:
#    twoBitMask micOch1.rmsk.2bit \
#        -add bed/simpleRepeat/trfMask.bed micOch1.2bit
    #   you can safely ignore the warning about fields >= 13
    twoBitToFa micOch1.2bit stdout | faSize stdin > faSize.micOch1.2bit.txt
    cat faSize.micOch1.2bit.txt
# 2287340943 bases (183019268 N's 2104321675 real 1601638277 upper
#	502683398 lower) in 6335 sequences in 1 files
# Total size: mean 361064.1 sd 4482029.3 min 1000 (chrUn_AHZW01186948)
#	max 126672627 (chr1) median 2515
# %21.98 masked total, %23.89 masked real

    rm /gbdb/micOch1/micOch1.2bit
    ln -s `pwd`/micOch1.2bit /gbdb/micOch1/micOch1.2bit

#########################################################################
# CREATE MICROSAT TRACK (DONE - 2017-01-25 - Hiram)
    ssh hgwdev
    mkdir /cluster/data/micOch1/bed/microsat
    cd /cluster/data/micOch1/bed/microsat

    awk '($5==2 || $5==3) && $6 >= 15 && $8 == 100 && $9 == 0 {printf("%s\t%s\t%s\t%dx%s\n", $1, $2, $3, $6, $16);}' \
       ../simpleRepeat/simpleRepeat.bed > microsat.bed

    hgLoadBed micOch1 microsat microsat.bed
    # Read 127857 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2013-06-07 - Hiram)

    mkdir /hive/data/genomes/micOch1/bed/windowMasker
    cd /hive/data/genomes/micOch1/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev micOch1) > do.log 2>&1
    # real    165m20.954s

    # Masking statistics
    cat faSize.micOch1.cleanWMSdust.txt
# 2287340943 bases (183019268 N's 2104321675 real 1478898175 upper
#	625423500 lower) in 6335 sequences in 1 files
# Total size: mean 361064.1 sd 4482029.3 min 1000 (chrUn_AHZW01186948)
#	max 126672627 (chr1) median 2515
# %27.34 masked total, %29.72 masked real

    cat fb.micOch1.rmsk.windowmaskerSdust.txt
    # 251778480 bases of 2287340943 (11.007%) in intersection

    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -continue=load -debug -dbHost=hgwdev micOch1) > load.log 2>&1

##########################################################################
# run up idKeys files for ncbiRefSeq (DONE - 2016-05-05 - Hiram)
    mkdir /hive/data/genomes/micOch1/bed/idKeys
    cd /hive/data/genomes/micOch1/bed/idKeys

    time (doIdKeys.pl -buildDir=`pwd`  micOch1) > do.log 2>&1
    # real    22m47.114s

    cat micOch1.keySignature.txt
    #   2869962b2f1b8aed754cf95e5febdd2a

##########################################################################
# cpgIslands - (DONE - 2013-11-25 - Hiram)
    mkdir /hive/data/genomes/micOch1/bed/cpgIslands
    cd /hive/data/genomes/micOch1/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku micOch1) > run.log 2>&1
    # Elapsed time: 6m48s

    cat fb.micOch1.cpgIslandExt.txt
    # 11062898 bases of 2104321675 (0.526%) in intersection

##############################################################################
# genscan - (DONE - 2013-09-11 - Hiram)
    mkdir /hive/data/genomes/micOch1/bed/genscan
    cd /hive/data/genomes/micOch1/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku micOch1) > do.log 2>&1
    # real    595m22.318s
# Completed: 6331 of 6335 jobs
# Crashed: 4 jobs
# CPU time in finished jobs:      62384s    1039.74m    17.33h    0.72d  0.002 y
# IO & Wait Time:                 17010s     283.49m     4.72h    0.20d  0.001 y
# Average job time:                  13s       0.21m     0.00h    0.00d
# Longest finished job:            3161s      52.68m     0.88h    0.04d
# Submission to last job:          3727s      62.12m     1.04h    0.04d

    # four jobs completed with window=2000000
./lastRunGsBig.csh chrUn_JH996442 000 gtf/000/chrUn_JH996442.gtf pep/000/chrUn_JH996442.pep subopt/000/chrUn_JH996442.bed &
./lastRunGsBig.csh chr10 000 gtf/000/chr10.gtf pep/000/chr10.pep subopt/000/chr10.bed &
./lastRunGsBig.csh chr18 000 gtf/000/chr18.gtf pep/000/chr18.pep subopt/000/chr18.bed &
./lastRunGsBig.csh chr1 000 gtf/000/chr1.gtf pep/000/chr1.pep subopt/000/chr1.bed
    # continuing:
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -continue=makeBed -bigClusterHub=ku micOch1) > makeBed.log 2>&1
    #  Elapsed time: 3m23s

    cat fb.micOch1.genscan.txt
    # 58244164 bases of 2104321675 (2.768%) in intersection

    cat fb.micOch1.genscanSubopt.txt
    # 56202479 bases of 2104321675 (2.671%) in intersection

#########################################################################
# Create kluster run files (DONE - 2017-01-25 - Hiram)

    # numerator is micOch1 gapless bases "real" as reported by:
    featureBits -noRandom -noHap micOch1 gap
    # 112230976 bases of 1543152531 (7.273%) in intersection
    #                     ^^^

    # denominator is hg19 gapless bases as reported by:
    #   featureBits -noRandom -noHap hg19 gap
    #     234344806 bases of 2861349177 (8.190%) in intersection
    # 1024 is threshold used for human -repMatch:
    calc \( 1543152531 / 2861349177 \) \* 1024
    #  ( 1543152531 / 2861349177 ) * 1024 = 552.252834

    # ==> use -repMatch=500 according to size scaled down from 1024 for human.
    #   and rounded down to nearest 50 approximately
    cd /hive/data/genomes/micOch1
    blat micOch1.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/micOch1.11.ooc \
        -repMatch=500
    #   Wrote 49691 overused 11-mers to jkStuff/micOch1.11.ooc

    #   check non-bridged gaps to see what the typical size is:
    hgsql -N \
        -e 'select * from gap where bridge="no" order by size;' micOch1 \
        | sort -k7,7nr | ave -col=7 stdin
    # all these gap sizes are 100
    # minimum gap size is 100 and produces a reasonable number of lifts
    gapToLift -verbose=2 -minGap=10 micOch1 jkStuff/nonBridged.lft \
        -bedFile=jkStuff/nonBridged.bed

########################################################################
# GENBANK AUTO UPDATE (DONE - 2017-01-25 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism             mrnaCnt   estCnt  refSeqCnt
    # Microtus ochrogaster    7       0       12

    # edit etc/genbank.conf to add micOch1 just before rheMac2
# micOch1 (prairie vole)
micOch1.serverGenome = /hive/data/genomes/micOch1/micOch1.2bit
micOch1.clusterGenome = /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.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
micOch1.downloadDir = micOch1
# micOch1.upstreamGeneTbl = refGene
# micOch1.upstreamMaf = multiz7way
# /hive/data/genomes/melGal4/bed/multiz7way/species.lst

    git commit -m "Added micOch1; refs #9871" etc/genbank.conf
    git push
    # update /cluster/data/genbank/:
    make etc-update

    # Edit src/lib/gbGenome.c to add new species.
    git commit -m "Added micOch1 Microtus ochrogaster - prairie vole refs #9871" \
       src/lib/gbGenome.c
    git push
    make install-server
    screen      #  control this business with a screen since it takes a while
    cd /cluster/data/genbank

    time ./bin/gbAlignStep -initial micOch1
    # logFile: var/build/logs/2017.01.25-19:53:43.micOch1.initalign.log
    #   real    806m16.270s

    tail var/build/logs/2017.01.25-19:53:43.micOch1.initalign.log
    #	hgwdev 2017.01.26-09:17:39 micOch1.initalign: Succeeded: micOch1
    #	hgwdev 2017.01.26-09:19:59 micOch1.initalign: finish

    #   To re-do, rm the dir first:
    #     /cluster/data/genbank/work/initial.micOch1

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad micOch1
    # logFile: var/dbload/hgwdev/logs/2017.01.26-10:30:14.micOch1.dbload.log
    #  real    17m58.909s

    tail -1 var/dbload/hgwdev/logs/2017.01.26-10:30:14.micOch1.dbload.log
    #  hgwdev 2017.01.26-10:48:12 micOch1.dbload: finish

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add micOch1 to:
    #   etc/align.dbs etc/hgwdev.dbs
    git add etc/align.dbs etc/hgwdev.dbs
    git commit -m 'adding micOch1 to the update alignments refs #9871' etc/align.dbs etc/hgwdev.dbs
    git push
    make etc-update

#############################################################################
# augustus gene track (DONE - 2015-05-20 - Hiram)

    mkdir /hive/data/genomes/micOch1/bed/augustus
    cd /hive/data/genomes/micOch1/bed/augustus
    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
        -species=human -dbHost=hgwdev \
           -workhorse=hgwdev micOch1) > do.log 2>&1
    # real    170m55.747s

    cat fb.micOch1.augustusGene.txt
    # 52632496 bases of 2104321675 (2.501%) in intersection

#########################################################################
#  BLATSERVERS ENTRY (DONE - 2017-01-26 - Hiram)
#	After getting a blat server assigned by the Blat Server Gods,
    ssh hgwdev

    hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("micOch1", "blat1d", "17880", "1", "0"); \
	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("micOch1", "blat1d", "17881", "0", "1");' \
	    hgcentraltest
    #	test it with some sequence

############################################################################
## reset default position to GULO gene (vitamin C)
##  (DONE - 2017-01-30 - Hiram)

    ssh hgwdev
    hgsql -e 'update dbDb set defaultPos="chr17:12364220-12405863"
	where name="micOch1";' hgcentraltest

#########################################################################
# all.joiner update, downloads and in pushQ - (DONE - 2017-01-30 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # fixup all.joiner until this is a clean output
    joinerCheck -database=micOch1 -tableCoverage all.joiner
    joinerCheck -database=micOch1 -times all.joiner
    joinerCheck -database=micOch1 -keys all.joiner

    cd /hive/data/genomes/micOch1
    time (makeDownloads.pl -workhorse=hgwdev micOch1) > downloads.log 2>&1
    #  real    22m13.021s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/micOch1/pushQ
    cd /hive/data/genomes/micOch1/pushQ
    time (makePushQSql.pl micOch1) > micOch1.pushQ.sql 2> stderr.out
    #  real    3m48.613s

    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: hgwdev does not have /gbdb/micOch1/wib/gc5Base.wib
    # WARNING: hgwdev does not have /gbdb/micOch1/wib/quality.wib
    # WARNING: hgwdev does not have /gbdb/micOch1/bbi/quality.bw
    # WARNING: micOch1 does not have seq
    # WARNING: micOch1 does not have extFile

    #   copy it to hgwbeta
    scp -p micOch1.pushQ.sql qateam@hgwbeta:/tmp/
    ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/micOch1.pushQ.sql"

    #   in that pushQ entry walk through each entry and see if the
    #   sizes will set properly

#########################################################################