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

# This file describes browser build for the ce11
# C. elegans equivalent to WS245 sequence

# Assembly Name:  WBcel235
# Organism name:  Caenorhabditis elegans
# Taxid:          6239
# Submitter:      C. elegans Sequencing Consortium
# Date:           2013-2-7
# BioSample:      SAMEA3138177
# Assembly type:  haploid
# Release type:   major
# Assembly level: Chromosome
# Genome representation: full
# GenBank Assembly Accession: GCA_000002985.3 (latest)
# RefSeq Assembly Accession: GCF_000002985.6 (species-representative latest)
# RefSeq Assembly and GenBank Assemblies Identical: no
#
## Assembly-Units:
## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
## GCA_000001175.3      GCF_000001175.4 Primary Assembly
##      GCF_000006485.1 non-nuclear

# separate Genbank chrMt sequence X54252.1 will be added

#############################################################################
# fetch sequence (DONE - 2015-06-10 - Hiram)
    mkdir -p /hive/data/genomes/ce11/genbank
    cd /hive/data/genomes/ce11/genbank

    rsync -L -a -P \
rsync://ftp.ncbi.nlm.nih.gov/genomes/genbank/invertebrate/Caenorhabditis_elegans/all_assembly_versions/GCA_000002985.3_WBcel235/ ./

    # measure what we have here:
    faCount GCA_000002985.3_WBcel235_genomic.fna.gz
#seq    len    A        C     G T     N cpg
BX284601.5 15072434     4835939 2695890 2692155 4848450 0       503518
BX284602.5 15279421     4878209 2769232 2762246 4869734 0       492142
BX284603.4 13783801     4444681 2449158 2466344 4423618 0       459676
BX284604.4 17493829     5711043 3034784 3017028 5730974 0       522372
BX284605.5 20924180     6750403 3712075 3701405 6760297 0       638988
BX284606.5 17718942     5747200 3119741 3117909 5734092 0       514719
total 100272607   32367475  17780880   17757087 32367165 0      3131415

#############################################################################
# fixup to UCSC naming scheme (DONE - 2015-06-10 - Hiram)
    mkdir /hive/data/genomes/ce11/ucsc
    cd /hive/data/genomes/ce11/ucsc

    ~/kent/src/hg/makeDb/doc/ce11/ucscCompositeAgp.pl \
../genbank/GCA_000002985.3_WBcel235_assembly_structure/Primary_Assembly

    # verify nothing lost compared to genbank:
    faCount *.fa
# #seq    len    A        C     G T     N cpg
# chrI    15072434        4835939 2695890 2692155 4848450 0       503518
# chrII   15279421        4878209 2769232 2762246 4869734 0       492142
# chrIII  13783801        4444681 2449158 2466344 4423618 0       459676
# chrIV   17493829        5711043 3034784 3017028 5730974 0       522372
# chrV    20924180        6750403 3712075 3701405 6760297 0       638988
# chrX    17718942        5747200 3119741 3117909 5734092 0       514719
# total   100272607   32367475  17780880 17757087 32367165   0    3131415

    # same numbers as above.

#############################################################################
#  Initial database build (DONE - 2015-02-15 - Hiram)

    cd /hive/data/genomes/ce11
    cat << '_EOF_' > ce11.config.ra
# Config parameters for makeGenomeDb.pl:
db ce11
# clade worm
# genomeCladePriority 10
scientificName Caenorhabditis elegans
commonName C. elegans
assemblyDate Aug. 2014
assemblyLabel Washington University School of Medicine GSC and Sanger Institute WBcel245
assemblyShortLabel WBcel245
orderKey 3024
mitoAcc X54252.1
fastaFiles /hive/data/genomes/ce11/ucsc/chr*.fa
agpFiles   /hive/data/genomes/ce11/ucsc/chr*.agp
# qualFiles /dev/null
dbDbSpeciesDir worm
photoCreditURL http://www.nematodes.org/
photoCreditName Photo courtesy of Mark Blaxter
ncbiGenomeId 41
ncbiAssemblyId 554278
ncbiAssemblyName WBcel245
ncbiBioProject 13758
genBankAccessionID GCA_000002985.3
taxId 6239
'_EOF_'
    # << happy emacs

    # verify sequence and AGP are OK:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -stop=agp ce11.config.ra) > agp.log 2>&1
    #  real    0m16.707s

    # verify end of agp.log indicates:
    # *** All done!  (through the 'agp' step)

    # then finish it off:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db ce11.config.ra) > db.log 2>&1
    # real    1m2.018s

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

##########################################################################
# running repeat masker (DONE - 2015-06-10 - Hiram)
    mkdir /hive/data/genomes/ce11/bed/repeatMasker
    cd /hive/data/genomes/ce11/bed/repeatMasker
    time (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku ce11) > do.log 2>&1
    # real    23m54.865s

    cat faSize.rmsk.txt
# 100286401 bases (0 N's 100286401 real 87767736 upper 12518665 lower)
#    in 7 sequences in 1 files
# Total size: mean 14326628.7 sd 6729073.3 min 13794 (chrM)
#    max 20924180 (chrV) median 15279421
# %12.48 masked total, %12.48 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 ce11 rmsk
    #  12518665 bases of 100286401 (12.483%) in intersection
    # real    1m27.493s

    # this one is actually not different as is the usual case, because
    #   there are no N's in this sequence.
    # why is it different than the faSize above ?
    # because rmsk masks out some N's as well as bases, the count above
    #   separates out the N's from the bases, it doesn't show lower case N's

##########################################################################
# running simple repeat (DONE - 2015-06-10 - Hiram)

    mkdir /hive/data/genomes/ce11/bed/simpleRepeat
    cd /hive/data/genomes/ce11/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        ce11) > do.log 2>&1
    # XXX did not finish successfully, failed in the clean step
    #  because there was no TrfPart hierarchy constructed
    # real    14m28.299s

    cat fb.simpleRepeat
    # 4381783 bases of 100286401 (4.369%) in intersection

    # add to rmsk after it is done:
    cd /hive/data/genomes/ce11
    twoBitMask ce11.rmsk.2bit \
        -add bed/simpleRepeat/trfMask.bed ce11.2bit
    #   you can safely ignore the warning about fields >= 13
    twoBitToFa ce11.2bit stdout | faSize stdin > faSize.ce11.2bit.txt
    cat faSize.ce11.2bit.txt
    # 100286401 bases (0 N's 100286401 real 87628173 upper 12658228 lower)
    #    in 7 sequences in 1 files
    # Total size: mean 14326628.7 sd 6729073.3 min 13794 (chrM)
    #    max 20924180 (chrV) median 15279421
    # %12.62 masked total, %12.62 masked real

    rm /gbdb/ce11/ce11.2bit
    ln -s `pwd`/ce11.2bit /gbdb/ce11/ce11.2bit

##########################################################################
## WINDOWMASKER (DONE - 2015-06-10 - Hiram)

    mkdir /hive/data/genomes/ce11/bed/windowMasker
    cd /hive/data/genomes/ce11/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev ce11) > do.log 2>&1
    # real    4m1.090s

    # Masking statistics
    cat faSize.ce11.cleanWMSdust.txt
    # 100286401 bases (0 N's 100286401 real 63460102 upper 36826299 lower)
    #    in 7 sequences in 1 files
    # Total size: mean 14326628.7 sd 6729073.3 min 13794 (chrM)
    #    max 20924180 (chrV) median 15279421
    #  %36.72 masked total, %36.72 masked real

    cat fb.ce11.rmsk.windowmaskerSdust.txt
    # 8688859 bases of 100286401 (8.664%) in intersection

##########################################################################
# cpgIslands - (DONE - 2015-06-10 - Hiram)
    mkdir /hive/data/genomes/ce11/bed/cpgIslands
    cd /hive/data/genomes/ce11/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku ce11) > do.log 2>&1 &
    # real    1m22.721s

    cat fb.ce11.cpgIslandExt.txt
    # 1092956 bases of 100286401 (1.090%) in intersection

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2015-06-10 - Hiram)
    mkdir /hive/data/genomes/ce11/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/ce11/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/ce11/ce11.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku ce11) > do.log 2>&1
    # Elapsed time: 0m52s

    cat fb.ce11.cpgIslandExtUnmasked.txt
    # 1406254 bases of 100286401 (1.402%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2015-06-10 - Hiram)
    mkdir /hive/data/genomes/ce11/bed/cytoBand
    cd /hive/data/genomes/ce11/bed/cytoBand
    makeCytoBandIdeo.csh ce11

#########################################################################
# augustus - (DONE - 2015-06-19 - Hiram)
    mkdir /hive/data/genomes/ce11/bed/augustus
    cd /hive/data/genomes/ce11/bed/augustus
    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
        -species=caenorhabditis -dbHost=hgwdev \
           -workhorse=hgwdev ce11) > do.log 2>&1
    # real    69m43.943s

    cat fb.ce11.augustusGene.txt
    # 25248650 bases of 100286401 (25.177%) in intersection

#########################################################################
# genscan - (DONE - 2015-06-10 - Hiram)
    mkdir /hive/data/genomes/ce11/bed/genscan
    cd /hive/data/genomes/ce11/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku ce11) > do.log 2>&1
    # real    10m10.946s

    cat fb.ce11.genscan.txt
    #   19205373 bases of 100286401 (19.151%) in intersection

    cat fb.ce11.genscanSubopt.txt
    #   118230 bases of 100286401 (0.118%) in intersection

########################################################################
# Create kluster run files (DONE - 2015-06-10 - Hiram)

    cd /hive/data/genomes/ce11
    # numerator is ce11 gapless bases "real" as reported by:
    head -1 faSize.ce11.2bit.txt
# 100286401 bases (0 N's 100286401 real 87628173 upper 12658228 lower)
#    in 7 sequences in 1 files

    # numerator is 'real' base count
    # 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 \( 100286401 / 2861349177 \) \* 1024
    # ( 100286401 / 2861349177 ) * 1024 = 35.889809

    # Use -repMatch=100 (based on size -- for human we use 1024, and
    # worm size is ~3.4% of human judging by gapless ce4 vs. hg18 genome
    # size from featureBits. So we would use 35, but that yields a very
    # high number of tiles to ignore, especially for a small more compact
    # genome.  Bump that up a bit to be more conservative.

    cd /hive/data/genomes/ce11
    time blat ce11.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/ce11.11.ooc \
        -repMatch=100
    # Wrote 8487 overused 11-mers to jkStuff/ce11.11.ooc
    #  real    0m1.897s

    # there are no non-bridged gaps, do not need to do this
    #   check non-bridged gaps to see what the typical size is:
#     hgsql -N -e 'select * from gap where bridge="no" order by size;' ce11
#       | ave -tableOut -col=7 stdin
# # min Q1 median Q3 max mean N sum stddev
# 50076 58368.8 70128 100495 1.07816e+07 178173 670 1.19376e+08 672006

    # note the minimum non-bridged gap size is 50,076

#  gapToLift -verbose=2 -minGap=50000 ce11 jkStuff/ce11.nonBridged.lft \
#         -bedFile=jkStuff/ce11.nonBridged.bed

#    hgsql -N \
#        -e 'select * from gap where bridge="no" order by size;' ce11 \
#        | ave -col=7 stdin

    # not needed:
#    gapToLift -verbose=2 -minGap=100 bosTau7 jkStuff/nonBridged.lft \
#        -bedFile=jkStuff/nonBridged.bed

    # survey sizes:
    n50.pl chrom.sizes
#       reading: chrom.sizes
#       contig count: 7, total size: 100286401, one half size: 50143200
# cumulative   N50 count      contig  contig size
# 38643122   2   chrX     17718942
# 50143200 one half size
# 56136951   3   chrIV    17493829

#############################################################################
# GENBANK AUTO UPDATE (DONE - 2015-06-10 - rerun 2016-01-22 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism       mrnaCnt estCnt  refSeqCnt
# Caenorhabditis afra     6       6       0
# Caenorhabditis angaria  7       0       0
# Caenorhabditis brenneri 180     30074   0
# Caenorhabditis briggsae 619     2424    0
# Caenorhabditis castelli 5       5       0
# Caenorhabditis doughertyi       6       6       0
# Caenorhabditis drosophilae      2       1       0
# Caenorhabditis elegans  9479    396692  27356
# Caenorhabditis elegans/Monacrosporium haptotylum mixed EST library      0       3936    0
# Caenorhabditis guadeloupensis   6       6       0
# Caenorhabditis imperialis       6       6       0
# Caenorhabditis japonica 9       33050   0
# Caenorhabditis kamaaina 8       8       0
# Caenorhabditis macrosperma      6       6       0
# Caenorhabditis nigoni   7       7       0
# Caenorhabditis nouraguensis     5       5       0
# Caenorhabditis plicata  2       1       0
# Caenorhabditis portoensis       6       6       0
# Caenorhabditis remanei  585     20292   0
# Caenorhabditis sp. 1 KK-2011    2       2       0
# Caenorhabditis sp. 2 KK-2011    2       1       0
# Caenorhabditis sp. 5 AC-2008    0       3868    0
# Caenorhabditis sp. 5 KK-2011    3       2       0
# Caenorhabditis sp. 8 KK-2011    4       2       0
# Caenorhabditis tropicalis       1       1       0
# Caenorhabditis virilis  5       5       0
# Caenorhabditis wallacei 7       7       0
# Caenorhabditis yunquensis       7       7       0

    # edit etc/genbank.conf to add ce11 just before ce10

# ce11 (C. elegans)
ce11.serverGenome = /hive/data/genomes/ce11/ce11.2bit
ce11.clusterGenome = /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

    git commit -m "Added ce11; refs #15209" etc/genbank.conf
    git push
    # update /cluster/data/genbank/:
    make etc-update

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

    # rerun all this with more tracks turned on 2016-01-21
    time ./bin/gbAlignStep -initial ce11
    # logFile: var/build/logs/2016.01.21-11:26:42.ce11.initalign.log
    # real    587m41.017s

    #   To re-do, rm the dir first:
    #     /cluster/data/genbank/work/initial.ce11

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad ce11 &
    # logFile: var/dbload/hgwdev/logs/2016.01.22-11:23:48.ce11.dbload.log
    # real    166m44.273s

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add ce11 to:
    #   vi etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added ce11 - C. elegans WS245 refs #15209" \
      etc/align.dbs etc/hgwdev.dbs
    git push
    make etc-update

#########################################################################
# ucscToINSDC table/track (DONE - 2015-06-10 - Hiram)
    mkdir /hive/data/genomes/ce11/bed/ucscToINSDC
    cd /hive/data/genomes/ce11/bed/ucscToINSDC

    grep chrM ../../ce11.agp
# chrM    1       13794   650     F       X54252.1        1       13794   +


    ~/kent/src/hg/utils/automation/ucscToINSDC.sh \
       ../../genbank/GCA_*assembly_structure/Primary_Assembly X54252.1

    awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \
         | sort > name.coordinate.tab
    join name.coordinate.tab ucscToINSDC.txt | tr '[ ]' '[\t]' \
         > ucscToINSDC.bed
    # verify all names are coming through, should be same line count:
    wc -l *
#   7 name.coordinate.tab
#   7 ucscToINSDC.bed
#   7 ucscToINSDC.txt

    cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1
    # 6
    # use the 6 in this sed
    sed -e "s/21/6/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
         | hgLoadSqlTab ce11 ucscToINSDC stdin ucscToINSDC.bed
    checkTableCoords ce11
    # should cover %100 entirely:
    featureBits -countGaps ce11 ucscToINSDC
    # 100286401 bases of 100286401 (100.000%) in intersection

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2015-06-10 - Hiram)
    hgsql -N -e "select frag from gold;" ce11 | sort -u \
        > /tmp/ce11.frag.gold.txt


    export maxLen=`awk '{print length($0)}' /tmp/ce11.frag.gold.txt | sort -rn | head -1`
    echo "scan to column: $maxLen"

export C=1
while [ $C -le $maxLen ];
do
echo -n " $C: "
awk '{ print substr($0,'$C',1) }' /tmp/ce11.frag.gold.txt | sort -u | xargs echo | sed -e 's/ //g'
C=`echo $C | awk '{print $1+1}'`
done
 1: ABCFXZ
 2: 123456789LOUX
 3: 0123456789
 4: 0123456789
 5: 0123456789
 6: 0123456789
 7: .0123456789
 8: 0123456789
 9: .
 10: 123456

    # verify this rule will find them all or eliminate them all:
    hgsql -N -e "select frag from gold;" ce11 | wc -l
    # 3268

    hgsql -N -e "select frag from gold;" ce11 \
       | egrep -e '[ABCFXZ][123456789LOUX][0-9]+(\.[0-9]+)?' | wc -l
    # 3268

    hgsql -N -e "select frag from gold;" ce11 \
       | egrep -v -e '[ABCFXZ][123456789LOUX][0-9]+(\.[0-9]+)?' | wc -l
    # 0

    # hence, add to trackDb/worm/ce11/trackDb.ra
searchTable gold
shortCircuit 1
termRegex [ABCFXZ][123456789LOUX][0-9]+(\.[0-9]+)?
query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
searchPriority 8

#########################################################################
# all.joiner update, downloads and in pushQ - (TBD 2015-03-23 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # fixup all.joiner until this is a clean output
    joinerCheck -database=ce11 -tableCoverage all.joiner
    joinerCheck -database=ce11 -times all.joiner
    joinerCheck -database=ce11 -keys all.joiner

    cd /hive/data/genomes/ce11
    time makeDownloads.pl ce11 > downloads.log 2>&1
    # real    18m36.348s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/ce11/pushQ
    cd /hive/data/genomes/ce11/pushQ
    makePushQSql.pl ce11 > ce11.pushQ.sql 2> stderr.out
    #   check for errors in stderr.out, some are OK, e.g.:
# WARNING: hgwdev does not have /gbdb/ce11/wib/gc5Base.wib
# WARNING: hgwdev does not have /gbdb/ce11/wib/quality.wib
# WARNING: hgwdev does not have /gbdb/ce11/bbi/qualityBw/quality.bw
# WARNING: ce11 does not have seq
# WARNING: ce11 does not have extFile
# WARNING: ce11 does not have estOrientInfo
# WARNING: ce11 does not have mrnaOrientInfo

    # can not push the chain/nets
    egrep -v "Chain and Net|Chain/Net" ce11.pushQ.sql \
      > ce11.noChainNet.pushQ.sql

    #   copy it to hgwbeta
    scp -p ce11.noChainNet.pushQ.sql qateam@hgwbeta:/tmp/ce11.pushQ.sql
    ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/ce11.pushQ.sql"
    #   in that pushQ entry walk through each entry and see if the
    #   sizes will set properly
    #   pushQ ID: 007625

#########################################################################
# LIFTOVER TO ce6 (DONE - 2015-06-23 - Hiram )
    mkdir /hive/data/genomes/ce11/bed/blat.ce6.2015-06-23
    cd /hive/data/genomes/ce11/bed/blat.ce6.2015-06-23
    # -debug run to create run dir, preview scripts...
    doSameSpeciesLiftOver.pl \
	-buildDir=`pwd` \
	-bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
	-ooc=/hive/data/genomes/ce11/jkStuff/ce11.11.ooc -debug ce11 ce6
    # Real run:
    time (doSameSpeciesLiftOver.pl \
     -buildDir=`pwd` \
      -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
       -ooc=/hive/data/genomes/ce11/jkStuff/ce11.11.ooc ce11 ce6) > do.log 2>&1
    #  real    3m53.579s
    # verify it works on genome-test

#############################################################################
# LIFTOVER TO ce10 (DONE - 2015-06-23 - Hiram )
    mkdir /hive/data/genomes/ce11/bed/blat.ce10.2015-06-23
    cd /hive/data/genomes/ce11/bed/blat.ce10.2015-06-23
    # -debug run to create run dir, preview scripts...
    doSameSpeciesLiftOver.pl \
	-buildDir=`pwd` \
	-bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
	-ooc=/hive/data/genomes/ce11/jkStuff/ce11.11.ooc -debug ce11 ce10
    # Real run:
    time (doSameSpeciesLiftOver.pl \
     -buildDir=`pwd` \
      -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
       -ooc=/hive/data/genomes/ce11/jkStuff/ce11.11.ooc ce11 ce10) > do.log 2>&1
    #  real    3m23.330s
    # verify it works on genome-test

#############################################################################
# reset default position, same as ce4/ce6/ce9/ce10 on the ZC101 / unc-52 locus
#	(DONE - 2015-06-24 - Hiram)
    ssh hgwdev
    hgsql -e 'update dbDb set defaultPos="chrII:14646376-14667875"
	where name="ce11";' hgcentraltest
############################################################################
## blat server turned on (DONE - 2016-01-22 - 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 ("ce11", "blat1a", "17854", "1", "0"); \
	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("ce11", "blat1a", "17855", "0", "1");' \
	    hgcentraltest
    #	test it with some sequence

############################################################################
#CREATE MICROSAT TRACK (DONE - 2016-02-03 - Hiram)
    ssh hgwdev
    mkdir /cluster/data/ce11/bed/microsat
    cd /cluster/data/ce11/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 ce11 microsat microsat.bed

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