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

# This file describes browser build for the colAng1
# Organism name:  Colobus angolensis palliatus (Angolan colobus)

#  Must find the photograph first, can not continue until finding
#  the photograph.

#########################################################################
#  Initial steps, find photograph (DONE - 2016-06-13 - Hiram)

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

mkdir ~/kent/src/hg/makeDb/doc/colAng1
cd ~/kent/src/hg/makeDb/doc/colAng1

sed -e 's/orcOrc/colAng/g; s/OrcOrc/ColAng/g; s/DONE/TBD/g;' ../orcOrc1/initialBuild.txt > initialBuild.txt


mkdir -p /hive/data/genomes/colAng1/refseq
cd /hive/data/genomes/colAng1/refseq

rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Colobus_angolensis/all_assembly_versions/GCF_000951035.1_Cang.pa_1.0/ ./

# need to find the photo, check NCBI 'genome' page to see what photo they
# display, if they do not have one, can usually find a public domain photo
# in wikimedia commons: https://commons.wikimedia.org/wiki/Main_Page

mkdir /hive/data/genomes/colAng1/photo
cd /hive/data/genomes/colAng1/photo

# this photo from: Eric Kilby  https://www.flickr.com/people/8749778@N06
#  https://commons.wikimedia.org/wiki/File:Colobus_Monkey_Seated_(14393774092).jpg

wget --timestamping \
   "https://upload.wikimedia.org/wikipedia/commons/thumb/2/2a/Colobus_Monkey_Seated_%2814393774092%29.jpg/1024px-Colobus_Monkey_Seated_%2814393774092%29.jpg"

# cropped that photo with ImageMagic to eliminate some of the surrounding
#  border, then

convert -quality 80 -geometry 400x300 \
        crop_colobus.jpg Colobus_angolensis_palliatus.jpg

# check this Colobus_angolensis_palliatus.jpg into
#    ~/kent/src/hg/htdocs/images/
# and copy that to /usr/local/apache/htdocs/images/

# construct the required photoReference.txt
cd /hive/data/genomes/colAng1
printf "photoCreditURL https://www.flickr.com/photos/ekilby/14393774092/
photoCreditName Eric Kilby (flickr)\n" > photoReference.txt


# this information is from the top of 
#    refseq/*_assembly_report.txt
#    (aka: refseq/GCF_000951035.1_Cang.pa_1.0_assembly_report.txt)

# Assembly name:  Cang.pa_1.0
# Organism name:  Colobus angolensis palliatus (Angolan colobus)
# Isolate:  OR3802
# Sex:  female
# Taxid:          336983
# BioSample:      SAMN03121814
# BioProject:     PRJNA279495
# Submitter:      Baylor College of Medicine
# Date:           2015-3-12
# Assembly type:  haploid
# Release type:   major
# Assembly level: Scaffold
# Genome representation: full
# WGS project:    JYKR01
# Assembly method: AllPathsLG v. 48744; Atlas Link v. 1.1; Atlas GapFill v.
# 2.2
# Genome coverage: 86.8x
# Sequencing technology: Illumina
# RefSeq category: Representative Genome
# GenBank assembly accession: GCA_000951035.1
# RefSeq assembly accession: GCF_000951035.1
# RefSeq assembly and GenBank assemblies identical: yes
#
## Assembly-Units:
## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
## GCA_000951065.1      GCF_000951065.1 Primary Assembly

#############################################################################
# establish config.ra file (DONE - Hiram - 2016-06-15)
    cd /hive/data/genomes/colAng1
    ~/kent/src/hg/utils/automation/prepConfig.pl colAng1 mammal \
      oldWorldMonkeys ./refseq/*_assembly_report.txt > colAng1.config.ra
# going to need a mitoAcc ?
    # edit result to add note about mito sequence

    # verify it looks sane
    cat colAng1.config.ra
# config parameters for makeGenomeDb.pl:
db colAng1
clade mammal
genomeCladePriority 35
scientificName Colobus angolensis palliatus
commonName Angolan colobus
assemblyDate Mar. 2015
assemblyLabel Baylor College of Medicine
assemblyShortLabel Cang.pa_1.0
orderKey 1505
# there is a mitochondrial sequence, but is indicated in genbank as
# unconfirmed KT626001.1
mitoAcc none
fastaFiles /hive/data/genomes/colAng1/ucsc/*.fa.gz
agpFiles /hive/data/genomes/colAng1/ucsc/*.agp
# qualFiles none
dbDbSpeciesDir oldWorldMonkeys
photoCreditURL https://www.flickr.com/photos/ekilby/14393774092/
photoCreditName Eric Kilby (flickr)
ncbiGenomeId 36539
ncbiAssemblyId 311101
ncbiAssemblyName Cang.pa_1.0
ncbiBioProject 279495
ncbiBioSample SAMN03121814
genBankAccessionID GCF_000951035.1
taxId 336983

#############################################################################
# setup UCSC named files (DONE - 2016-06-15 - Hiram)

    mkdir /hive/data/genomes/colAng1/ucsc
    cd /hive/data/genomes/colAng1/ucsc
    # measure what is in the refseq release:
    faSize ../refseq/*0_genomic.fna.gz
# 2970124662 bases (290151526 N's 2679973136 real 1742869490 upper
#    937103646 lower) in 13124 sequences in 1 files
# Total size: mean 226312.5 sd 1445798.8 min 1000 (NW_012122403.1)
#    max 35326507 (NW_012118487.1) median 3162
# %31.55 masked total, %34.97 masked real

    # check for duplicate sequences:

    time faToTwoBit -noMask ../refseq/*0_genomic.fna.gz refseq.2bit
    #  real    1m13.425s

    twoBitDup refseq.2bit
    # no output is a good result, otherwise, would have to eliminate duplicates

    # no mito sequence to use, otherwise would fix it up here

    # since this is all unplaced scaffold sequence, merely fixup the .1 names
    # simple conversion of names .1 to v1
    zcat ../refseq/*_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \
        | sed -e 's/.1\t/v1\t/;' > ucsc.agp

    zcat ../refseq/*_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \
        | sed -e 's/.1 Colobus.*/v1/;' | gzip > ucsc.fa.gz

    # verify correspondence
    time faToTwoBit *.fa.gz test.2bit
    # real    1m19.049s

    cat *.agp | checkAgpAndFa stdin test.2bit 2>&1 | tail
    # All AGP and FASTA entries agree - both files are valid

    # no longer need these 2bit files
    rm test.2bit refseq.2bit

#############################################################################
#  Initial database build (DONE - 2016-06-15 - Hiram)

    # verify sequence and AGP are OK:
    cd /hive/data/genomes/colAng1
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -stop=seq colAng1.config.ra) > seq.log 2>&1
    # real    2m18.688s
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -continue=agp -stop=agp colAng1.config.ra) > agp.log 2>&1
    # real    0m21.077s
    # then finish it off:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db colAng1.config.ra) > db.log 2>&1
    # real    21m48.313s

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

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2016-06-15 - Hiram)
    mkdir /hive/data/genomes/colAng1/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/colAng1/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/colAng1/colAng1.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku colAng1) > do.log 2>&1
    # real    6m43.150s

    cat fb.colAng1.cpgIslandExtUnmasked.txt
    # 24367499 bases of 2679973137 (0.909%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2016-06-15 - Hiram)
    mkdir /hive/data/genomes/colAng1/bed/cytoBand
    cd /hive/data/genomes/colAng1/bed/cytoBand
    makeCytoBandIdeo.csh colAng1

#############################################################################
# ucscToINSDC table/track (DONE - 2016-06-15 - Hiram)
    # the sequence here is working for a 'refseq' assembly *without* a chrM
    # situation may be specific depending upon what is available in the assembly

    mkdir /hive/data/genomes/colAng1/bed/ucscToINSDC
    cd /hive/data/genomes/colAng1/bed/ucscToINSDC

    ~/kent/src/hg/utils/automation/ucscToINSDC.sh \
        ../../refseq/GCF_*structure/Primary_Assembly
    awk '{printf "%s\t%s\n", $2, $1}' ucscToINSDC.txt | sort > insdcToUcsc.txt

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

    awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \
         | sort > name.coordinate.tab

    # the tr commands avoid the problem of trying to use the -t argument
    # to the join command which doesn't accept -t'\t' but instead has
    # to use the unseen/can not copy command ctrl-v i
    join insdc.refseq.txt insdcToUcsc.txt | tr '[ ]' '[\t]' | sort -k3 \
       | join -2 3 name.coordinate.tab - | tr '[ ]' '[\t]' | cut -f1-3,5 \
           > ucscToINSDC.bed

    # should be same line counts throughout:
    wc -l *
    #  13124 insdc.refseq.txt
    #  13124 insdcToUcsc.txt
    #  13124 name.coordinate.tab
    #  13124 ucscToINSDC.bed
    #  13124 ucscToINSDC.txt

    cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1
    # 14
    # use the 14 in this sed
    sed -e "s/21/14/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
         | hgLoadSqlTab colAng1 ucscToINSDC stdin ucscToINSDC.bed
    checkTableCoords colAng1
    # should cover %100 entirely:
    featureBits -countGaps colAng1 ucscToINSDC
    # 2970124662 bases of 2970124662 (100.000%) in intersection

    join -1 2 <(sort -k2 ucscToINSDC.txt) insdc.refseq.txt | tr '[ ]' '[\t]' \
      | sort -k2 | join -2 2 name.coordinate.tab - |  tr '[ ]' '[\t]' \
        | cut -f1-4 > ucscToRefSeq.bed
    cut -f1 ucscToRefSeq.bed | awk '{print length($0)}' | sort -n | tail -1
    # 14
    # use the 14 in this sed
    sed -e "s/21/14/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
       | sed -e 's/INSDC/RefSeq/g;' > ucscToRefSeq.sql
    hgLoadSqlTab colAng1 ucscToRefSeq ./ucscToRefSeq.sql ucscToRefSeq.bed

    checkTableCoords  colAng1 -table=ucscToRefSeq
    # should cover %100 all bases:
    featureBits -countGaps colAng1 ucscToRefSeq
    # 2970124662 bases of 2970124662 (100.000%) in intersection

#########################################################################
# add chromAlias table (DONE - 2017-12-13 - Hiram)

    mkdir /hive/data/genomes/colAng1/bed/chromAlias
    cd /hive/data/genomes/colAng1/bed/chromAlias

    hgsql -N -e 'select chrom,name from ucscToRefSeq;' colAng1 \
        > ucsc.refseq.tab
    hgsql -N -e 'select chrom,name from ucscToINSDC;' colAng1 \
        | grep -v chrM > ucsc.genbank.tab

    join -t$'\t' ../idKeys/colAng1.idKeys.txt \
	../../ensembl/ensemblColAng1.idKeys.txt \
	| cut -f2,3 | sort > ucsc.ensembl.tab

    ~/kent/src/hg/utils/automation/chromAlias.pl
    sort -o colAng1.chromAlias.tab colAng1.chromAlias.tab

for t in refseq genbank ensembl
do
  c0=`cat ucsc.$t.tab | wc -l`
  c1=`grep $t colAng1.chromAlias.tab | wc -l`
  ok="OK"
  if [ "$c0" -ne "$c1" ]; then
     ok="ERROR"
  fi
  printf "# checking $t: $c0 =? $c1 $ok\n"
done
# checking refseq: 13124 =? 13124 OK
# checking genbank: 13124 =? 13124 OK
# checking ensembl: 13124 =? 13124 OK

    hgLoadSqlTab colAng1 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
        colAng1.chromAlias.tab

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2017-02-01 - Hiram)

    cd ~/kent/src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1
    # preview prefixes and suffixes:
    hgsql -N -e "select frag from gold;" colAng1 \
      | sed -e 's/[0-9][0-9]*//;' | sort | uniq -c 
#  197124 JYKR.1

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

    # verify this rule will find them all or eliminate them all:
    hgsql -N -e "select frag from gold;" colAng1 | wc -l
    # 197124

    hgsql -N -e "select frag from gold;" colAng1 \
       | egrep -e 'JYKR[0-9]+(\.[0-9]+)?' | wc -l
    # 197124

    hgsql -N -e "select frag from gold;" colAng1 \
       | egrep -v -e 'JYKR[0-9]+(\.[0-9]+)?' | wc -l
       | egrep -v -e '[ACLNO_]+[0-9]+(\.[0-9]+)?' | wc -l
    # 0

    # hence, add to trackDb/oldWorldMonkeys/colAng1/trackDb.ra
searchTable gold
shortCircuit 1
termRegex JYKR[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 - 2016-06-15 - Hiram)
    mkdir /hive/data/genomes/colAng1/bed/repeatMasker
    cd /hive/data/genomes/colAng1/bed/repeatMasker
    time  (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku colAng1) > do.log 2>&1
    # real    971m47.129s


    cat faSize.rmsk.txt
# 2970124662 bases (290151526 N's 2679973136 real 1348602558 upper
#    1331370578 lower) in 13124 sequences in 1 files
# Total size: mean 226312.5 sd 1445798.8 min 1000 (NW_012122403v1)
#    max 35326507 (NW_012118487v1) median 3162
# %44.83 masked total, %49.68 masked real

    egrep -i "versi|relea" do.log
    # RepeatMasker version open-4.0.5
    #    January 31 2015 (open-4-0-5) version of RepeatMasker
    # CC   RELEASE 20140131;

    time featureBits -countGaps colAng1 rmsk
    # 1333003423 bases of 2970124662 (44.880%) in intersection
    # real    0m51.170s

    # 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

    # with high contig count assemblies, faster way to get a similar result:
    time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' colAng1 \
        | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total"
    # total 1333003423.000000
    # real    0m37.908s

##########################################################################
# running simple repeat (DONE - 2016-06-15 - Hiram)

    mkdir /hive/data/genomes/colAng1/bed/simpleRepeat
    cd /hive/data/genomes/colAng1/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        colAng1) > do.log 2>&1
    # real    6m4.160s

    cat fb.simpleRepeat
    # 61072817 bases of 2679973137 (2.279%) in intersection

    # add to rmsk after it is done:
    cd /hive/data/genomes/colAng1
    twoBitMask colAng1.rmsk.2bit \
        -add bed/simpleRepeat/trfMask.bed colAng1.2bit
    #   you can safely ignore the warning about fields >= 13
    twoBitToFa colAng1.2bit stdout | faSize stdin > faSize.colAng1.2bit.txt
    cat faSize.colAng1.2bit.txt
# 2970124662 bases (290151526 N's 2679973136 real 1347488473 upper
#    1332484663 # lower) in 13124 sequences in 1 files
# Total size: mean 226312.5 sd 1445798.8 min 1000 (NW_012122403v1)
#    max 35326507 (NW_012118487v1) median 3162
# %44.86 masked total, %49.72 masked real

    rm /gbdb/colAng1/colAng1.2bit
    ln -s `pwd`/colAng1.2bit /gbdb/colAng1/colAng1.2bit

#########################################################################
# CREATE MICROSAT TRACK (DONE - 2016-06-17 - Hiram)
    ssh hgwdev
    mkdir /cluster/data/colAng1/bed/microsat
    cd /cluster/data/colAng1/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 colAng1 microsat microsat.bed
    # Read 20365 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2016-06-17 - Hiram)

    mkdir /hive/data/genomes/colAng1/bed/windowMasker
    cd /hive/data/genomes/colAng1/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev colAng1) > do.log 2>&1
    #  real    255m31.780s

    # Masking statistics
    cat faSize.colAng1.cleanWMSdust.txt
# 2970124662 bases (290151526 N's 2679973136 real 1728634448 upper
#    951338688 lower) in 13124 sequences in 1 files
# Total size: mean 226312.5 sd 1445798.8 min 1000 (NW_012122403v1)
#    max 35326507 (NW_012118487v1) median 3162
# %32.03 masked total, %35.50 masked real

    cat fb.colAng1.rmsk.windowmaskerSdust.txt
    # 726653964 bases of 2970124662 (24.465%) in intersection

#########################################################################
# run up idKeys files for ncbiRefSeq (DONE - 2016-06-17 - Hiram)
    mkdir /hive/data/genomes/colAng1/bed/idKeys
    cd /hive/data/genomes/colAng1/bed/idKeys

    time (doIdKeys.pl -buildDir=`pwd`  colAng1) > do.log 2>&1
    # real    12m32.106s

    cat colAng1.keySignature.txt
    #   d75c00e0e61c84d9ac35edcf1437d4f4

##########################################################################
# ncbiRefSeq - (DONE - 2016-06-17 - Hiram)
    # must have previously run idKeys
    mkdir /hive/data/genomes/colAng1/bed/ncbiRefSeq
    cd /hive/data/genomes/colAng1/bed/ncbiRefSeq
    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl \
       -buildDir=`pwd` -bigClusterHub=ku -dbHost=hgwdev \
-stop=download \
      -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
        refseq vertebrate_mammalian Colobus_angolensis \
          GCF_000951035.1_Cang.pa_1.0 colAng1) > download.log 2>&1
    # real    14m38.791s
    # lost the download.log

    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl \
       -buildDir=`pwd` -bigClusterHub=ku -dbHost=hgwdev \
-continue=process -stop=process \
      -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
        refseq vertebrate_mammalian Colobus_angolensis \
          GCF_000951035.1_Cang.pa_1.0 colAng1) > process.log 2>&1
    # real    2m27.949s

    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl \
       -buildDir=`pwd` -bigClusterHub=ku -dbHost=hgwdev \
-continue=load -stop=load \
      -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
        refseq vertebrate_mammalian Colobus_angolensis \
          GCF_000951035.1_Cang.pa_1.0 colAng1) > load.log 2>&1
    # real    0m23.690s

    featureBits -countGaps colAng1 ncbiRefSeq
# 64656476 bases of 2970124662 (2.177%) in intersection

##########################################################################
# cpgIslands - (DONE - 2016-06-17 - Hiram)
    mkdir /hive/data/genomes/colAng1/bed/cpgIslands
    cd /hive/data/genomes/colAng1/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku colAng1) > do.log 2>&1
    #   real    6m59.048s

    cat fb.colAng1.cpgIslandExt.txt
    # 14582855 bases of 2679973137 (0.544%) in intersection

##############################################################################
# genscan - (DONE - 2016-06-17 - Hiram)
    mkdir /hive/data/genomes/colAng1/bed/genscan
    cd /hive/data/genomes/colAng1/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku colAng1) > do.log 2>&1
    # real    32m12.877s

    cat fb.colAng1.genscan.txt
    # 49704578 bases of 2679973137 (1.855%) in intersection

    cat fb.colAng1.genscanSubopt.txt
    # 51121942 bases of 2679973137 (1.908%) in intersection

########################################################################
# Create kluster run files (DONE - 2016-06-17 - Hiram)

    cd /hive/data/genomes/colAng1
    # numerator is colAng1 gapless bases "real" as reported by:
    head -1 faSize.colAng1.2bit.txt
# 2970124662 bases (290151526 N's 2679973136 real 1347488473 upper 1332484663 lower) in 13124 sequences in 1 files

    # if there were lots of randoms and haplotypes:
    # featureBits -noRandom -noHap colAng1 gap
    # 290151525 bases of 2679973137 (10.827%) 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 \( 2679973136 / 2861349177 \) \* 1024
    #  ( 2679973136 / 2861349177 ) * 1024 = 959.090388

    # ==> use -repMatch=900 according to size scaled down from 1024 for human.
    #   and rounded down to nearest 50
    blat colAng1.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/colAng1.11.ooc \
        -repMatch=900
    #   Wrote 29536 overused 11-mers to jkStuff/colAng1.11.ooc


    # there are no non-bridged gaps
    hgsql -e 'select count(*) from gap;' colAng1
# +----------+
# | count(*) |
# +----------+
# |   184000 |
# +----------+

    hgsql -e 'select count(*) from gap where bridge="no";' colAng1
# +----------+
# | count(*) |
# +----------+
# |        0 |
# +----------+

    # if there were non-bridged gaps, make up a nonBridged.lft file

    #   check non-bridged gaps to see what the typical size is:
#    hgsql -N \
#         -e 'select * from gap where bridge="no" order by size;' colAng1 \
#         | sort -k7,7nr | ave -col=7 stdin
    #   most non-bridged gaps have size = 100
    #   decide on a minimum gap for this break, use either 100 or 5000 will
    #   generate 13387 liftOver rows, but if use 6000, only got 11703 rows.
    #   so use 100 here to get more liftOver row.
#     gapToLift -verbose=2 -minGap=100 colAng1 jkStuff/nonBridged.lft \
#         -bedFile=jkStuff/nonBridged.bed

########################################################################
# GENBANK AUTO UPDATE (DONE - 2017-02-01 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism     mrnaCnt estCnt  refSeqCnt
    # Colobus angolensis      1       0       0
    # Colobus angolensis palliatus    1       0       3
    # Colobus guereza 36      3       0
    # Colobus guereza kikuyuensis     2       0       0

    # Edit src/lib/gbGenome.c to add new species

    # edit etc/genbank.conf to add colAng1 just after balAcu1

# colAng1 (Colobus angolensis palliatus) (13,124 contigs, 86.6X coverage)
colAng1.serverGenome = /hive/data/genomes/colAng1/colAng1.2bit
colAng1.clusterGenome = /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.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

    git commit -m "Added colAng - Colobus angolensis palliatus - refs #17545" etc/genbank.conf src/lib/gbGenome.c
    git push
    # update /cluster/data/genbank/:
    make etc-update
    make install-server

    screen      #  control this business with a screen since it takes a while
    cd /cluster/data/genbank

    time ./bin/gbAlignStep -initial colAng1
    # logFile: var/build/logs/2016.10.25-10:48:28.colAng1.initalign.log

    tail -2 var/build/logs/2016.10.25-10:48:28.colAng1.initalign.log
# hgwdev 2016.10.26-19:04:18 colAng1.initalign: Succeeded: colAng1
# hgwdev 2016.10.26-19:05:15 colAng1.initalign: finish

    #   approximately 1,936 minutes == 32.3 hours

    #   To re-do, rm the dir first:
    #     /cluster/data/genbank/work/initial.colAng1

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad colAng1
    # logFile: var/dbload/hgwdev/logs/2017.02.01-11:42:06.colAng1.dbload.log

    # real    119m13.047s

    tail -1 var/dbload/hgwdev/logs/2017.02.01-11:42:06.colAng1.dbload.log
# hgwdev 2017.02.01-13:41:19 colAng1.dbload: finish

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add colAng1 to:
    #   etc/align.dbs etc/hgwdev.dbs
    git add etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added colAng1 - Angolan colobus - Colobus angolensis palliatus - refs #17545" etc/align.dbs etc/hgwdev.dbs
    git push
    make etc-update

#############################################################################
# augustus gene track (DONE - 2017-02-01 - Hiram)

    mkdir /hive/data/genomes/colAng1/bed/augustus
    cd /hive/data/genomes/colAng1/bed/augustus
    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
        -species=human -dbHost=hgwdev \
           -workhorse=hgwdev colAng1) > do.log 2>&1
    # real    103m43.099s

    cat fb.colAng1.augustusGene.txt
    # 45199098 bases of 2679973137 (1.687%) in intersection

#############################################################################
# chainNet swap from human/hg38 (DONE - 2017-02-27 - Hiram)

    # alignment on hg38
    cd /hive/data/genomes/hg38/bed/lastzColAng1.2017-02-27
    cat fb.hg38.chainColAng1Link.txt
    # 2489504237 bases of 3049335806 (81.641%) in intersection

    # running the swap
    mkdir /hive/data/genomes/colAng1/bed/blastz.hg38.swap
    cd /hive/data/genomes/colAng1/bed/blastz.hg38.swap
    time (doBlastzChainNet.pl -verbose=2 \
        -swap /hive/data/genomes/hg38/bed/lastzColAng1.2017-02-27/DEF \
        -chainMinScore=5000 -chainLinearGap=medium \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -syntenicNet) > swap.log 2>&1
    # real    80m23.924s

    cat fb.colAng1.chainHg38Link.txt
    # 2355021477 bases of 2679973137 (87.875%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        colAng1 hg38) > rbest.log 2>&1
    # real    224m29.002s

#############################################################################
# swap chainNet from mm10 (DONE - 2017-03-01 - Hiram)
    # since this is a new assembly, add the chainNet definitions to
    # trackDb

    # the original results
    cd /hive/data/genomes/mm10/bed/lastzColAng1.2017-02-28
    cat fb.mm10.chainColAng1Link.txt
    # 902325064 bases of 2652783500 (34.014%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/colAng1/bed/blastz.mm10.swap
    cd /hive/data/genomes/colAng1/bed/blastz.mm10.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/mm10/bed/lastzColAng1.2017-02-28/DEF \
        -swap -chainMinScore=3000 -chainLinearGap=medium \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    62m44.125s

    cat fb.colAng1.chainMm10Link.txt
    # 885418780 bases of 2679973137 (33.038%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` colAng1 mm10) \
       > rbest.log 2>&1
    # real    296m19.689s

#############################################################################
#  BLATSERVERS ENTRY (DONE - 2017-11-17 - 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 ("colAng1", "blat1a", "17882", "1", "0"); \
	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("colAng1", "blat1a", "17883", "0", "1");' \
	    hgcentraltest
    #	test it with some sequence

############################################################################
## default position to casein beta (CSN2) gene (milk production)
#                                 (DONE - 2017-02-27 - Hiram)
    ssh hgwdev
    hgsql -e 'update dbDb set defaultPos="NW_012120710v1:924956-934903"
	where name="colAng1";' hgcentraltest

#########################################################################
# all.joiner update, downloads and in pushQ - (DONE - 2017-02-03 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # fixup all.joiner until this is a clean output
    joinerCheck -database=colAng1 -tableCoverage all.joiner
    joinerCheck -database=colAng1 -times all.joiner
    joinerCheck -database=colAng1 -keys all.joiner

    cd /hive/data/genomes/colAng1
    time (makeDownloads.pl colAng1) > downloads.log 2>&1
    #  real    15m52.648s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/colAng1/pushQ
    cd /hive/data/genomes/colAng1/pushQ
    time (makePushQSql.pl colAng1) > colAng1.pushQ.sql 2> stderr.out
    #   real    11m56.179s

    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: hgwdev does not have /gbdb/colAng1/wib/gc5Base.wib
    # WARNING: hgwdev does not have /gbdb/colAng1/wib/quality.wib
    # WARNING: hgwdev does not have /gbdb/colAng1/bbi/quality.bw
    # WARNING: colAng1 does not have seq
    # WARNING: colAng1 does not have extFile

    #   copy it to hgwbeta
    scp -p colAng1.pushQ.sql qateam@hgwbeta:/tmp/
    ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/colAng1.pushQ.sql"

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

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