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

# 
# RED FLOUR BEETLE!!!
# Tribolium castaneum -- 2.0 assembly Oct 10, 2005
# 
# ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Tcastaneum/

# GET SEQUENCE / SET UP DIRS (DONE Andy 10/22/2005)
    ssh hgwdev
    cd /cluster/store9
    mkdir triCas2
    cd /cluster/data
    ln -s /cluster/store9/triCas2 triCas2
    cd triCas2
    mkdir downloads bed
    cd downloads/
    wget ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Tcastaneum/Tcas2.0/contigs/Tcas20050914-contigs
    wget ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Tcastaneum/Tcas2.0/contigs/Tcas20050914.agp
    sed 's/#.*//' Tcas20050914.agp > beetle.agp
    sed 's/^>gi|[0-9]\+|gb|\([0-9A-Z]\+\)\.1|.*/>\1/' Tcas20050914-contigs > contigs.fa
    agpAllToFaFile beetle.agp contigs.fa beetle.fa
    faSize beetle.fa 
#199682416 bases (48132453 N's 151549963 real 151549963 upper 0 lower) in 2211 sequences in 1 files
#Total size: mean 90313.2 sd 1137291.7 min 248 (singleUn_1093) max 32080666 (ChLG3) median 1526
#N count: mean 21769.5 sd 327170.2
#U count: mean 68543.6 sd 816613.0
#L count: mean 0.0 sd 0.0
    
# CREATING DATABASE (DONE 10/22/2005 Andy)
    ssh hgwdev
    hgsql '' -e 'create database triCas2'

# LOAD GAP & GOLD TABLES FROM AGP (DONE 10/22/2005 Andy)
    ssh hgwdev
    cd /cluster/data/triCas2/downloads
    hgGoldGapGl -noGl triCas2 beetle.agp
    hgsql triCas2 -e 'analyze table gold; analyze table gap;'

# REPEATMASKER (DONE 10/22/2005 Andy)
    ssh pk
    mkdir -p /SAN/rmsk/{splits,run,out}
    cd /SAN
    faSplit -outDirDepth=1 -lift=500kSplits/splits.lft gap /cluster/data/triCas2/downloads/beetle.fa 500000 500kSplits/beet_
    cd rmsk/
    ln -s ../500kSplits splits
    cd run/
    cat > rmsk.sh << "EOF"
#!/bin/bash
fa=`basename $1`
param=-spec Tenebrionoidea

pushd /scratch
oldDir=`dirs +1`
cp $oldDir/$1 .
/cluster/bluearc/RepeatMasker/RepeatMasker $param $fa
mkdir -p $oldDir/`dirname $2`
cp $fa.out $oldDir/$2
rm $fa*
popd
EOF
    chmod +x rmsk.sh
    cat > gsub << "EOF"
#LOOP
./rmsk.sh {check in line+ $(path1)} {check out exists ../out/$(lastDir)/$(file1).out} 
#ENDLOOP
EOF
    find ../splits/ -name '*.fa' > fa.lst
    gensub2 fa.lst single gsub spec
    para create spec
    para try
    para push
    para time
#Completed: 2572 of 2572 jobs
#CPU time in finished jobs:     610301s   10171.69m   169.53h    7.06d  0.019 y
#IO & Wait Time:                 61073s    1017.88m    16.96h    0.71d  0.002 y
#Average job time:                 261s       4.35m     0.07h    0.00d
#Longest running job:                0s       0.00m     0.00h    0.00d
#Longest finished job:            3063s      51.05m     0.85h    0.04d
#Submission to last job:          6465s     107.75m     1.80h    0.07d
    cd ../
    head -n 3 out/0/beet_010.fa.out > head
    find out/ -name "*.fa.out" -type f -size +80c -exec tail +4 '{}' ';' > tmp
    cat head tmp > tmp2
    liftUp rmsk.out splits/splits.lft warn tmp2
    rm head tmp tmp2
    ssh hgwdev
    cd /SAN/rmsk
    hgLoadOut triCas2 rmsk.out
    hgsql triCas2 -e 'rename table rmsk_rmsk to rmsk'
    hgsql triCas2 -e 'drop index bin       on rmsk; \
                  drop index genoStart on rmsk; \
                  drop index genoEnd   on rmsk; \
                  create index bin       on rmsk (genoName(11), bin); \
                  create index genoStart on rmsk (genoName(11), genoStart); \
                  create index genoEnd   on rmsk (genoName(11), genoEnd);' 
    rm splits
    cd ../
    cp -r rmsk/ /cluster/data/triCas2/bed

# SIMPLE REPEATS (TRF) (DONE 10/22/2005 Andy)
    ssh pk
    cd /SAN
    mkdir -p simpleRepeat/{run,out}
    cd simpleRepeat/
    ln -s ../500kSplits splits
    cd run/
    cat << "_EOF_" > gsub
#LOOP
./trfBig.sh {check in line+ $(path1)} {check out line+ ../out/$(lastDir1)/$(root1).bed}
#ENDLOOP
_EOF_
   cat << "_EOF_" > trfBig.sh
#!/bin/bash
outDir=`dirname $2`
outName=`basename $2`
inName=`basename $1`

mkdir -p $outDir
cp $1 /scratch
pushd /scratch
trfBig $inName $outName -bed -tempDir=/tmp > /dev/null
popd
cp /scratch/$outName $2
rm /scratch/$outName /scratch/$inName
_EOF_
    chmod +x trfBig.sh
    find ../splits/ -name '*.fa' > fa.lst
    gensub2 fa.lst single gsub spec
    para create spec
    para try
    para push
    para time
#Completed: 2572 of 2572 jobs
#CPU time in finished jobs:       2137s      35.62m     0.59h    0.02d  0.000 y
#IO & Wait Time:                  6493s     108.22m     1.80h    0.08d  0.000 y
#Average job time:                   3s       0.06m     0.00h    0.00d
#Longest running job:                0s       0.00m     0.00h    0.00d
#Longest finished job:             475s       7.92m     0.13h    0.01d
#Submission to last job:           908s      15.13m     0.25h    0.01d
    cd ../
    find out/ -name "*.bed" -type f -exec grep "^beet" '{}' ';' > tmp
    liftUp trf.bed splits/splits.lft warn tmp
    rm tmp
    ssh hgwdev
    cd SAN/simpleRepeat/
    hgLoadBed -sqlTable=/cluster/home/aamp/kent/src/hg/lib/simpleRepeat.sql \
       triCas2 simpleRepeat trf.bed    
    rm splits
    cd ../    
    cp -r simpleRepeat/ /cluster/data/triCas2/bed

# MAKE MASKED 2BIT (DONE 10/22/2005 Andy)
    # make a filtered version of the trf output keep trf's with period <= 12:
    ssh hgwdev
    cd /cluster/data/triCas2
    awk '{if ($5 <= 12) print;}' bed/simpleRepeat/trf.bed > trfMask.bed
    maskOutFa -soft downloads/beetle.fa trfMask.bed tmp
    maskOutFa -softAdd tmp bed/rmsk/rmsk.out beetle.masked.fa
    faToTwoBit beetle.masked.fa triCas2.2bit
    hgsql triCas2 < ~/kent/src/hg/lib/chromInfo.sql
    twoBitInfo triCas2.2bit /dev/stdout | 
        awk '{printf("%s\t%s\t/gbdb/triCas2/triCas2.2bit\n", $1, $2)}' > chrom.sizes
    echo "load data local infile 'chrom.sizes' into table chromInfo;" | hgsql triCas2

# CREATING GRP TABLE FOR TRACK GROUPING (DONE 10/22/2005 Andy)
    # Copy all the data from the table "grp" in an existing database to the new database
    ssh hgwdev
    hgsql triCas2 -e 'create table grp (PRIMARY KEY(NAME)) select * from hg17.grp'

# SOME GBDB STUFF (DONE 10/22/2005 Andy)
    ssh hgwdev
    mkdir -p /gbdb/triCas2
    mkdir /cluster/data/triCas2/html
    ln -s /cluster/data/triCas2/html /gbdb/triCas2/html
    ln -s /cluster/data/triCas2/triCas2.2bit /gbdb/triCas2/triCas2.2bit

# MAKE HGCENTRALTEST ENTRY AND TRACKDB TABLE (DONE 10/22/2005 Andy)
    ssh hgwdev
    hgsql -N hgcentraltest -e 'INSERT INTO dbDb \
        (name, description, nibPath, organism, \
             defaultPos, active, orderKey, genome, scientificName, \
             htmlPath, hgNearOk, hgPbOk, sourceName) values \
        ("triCas2", "Sept. 2005", "/gbdb/triCas2", "T. castaneum", \
             "ChLG4:2220000-2245000", 1, 58, \
             "T. castaneum", \
             "Tribolium castaneum", "/gbdb/triCas2/html/description.html", \
             0, 0, "Baylor");'
    hgsql -N hgcentraltest -e 'delete from defaultDb where name="triCas1"'
    hgsql -N hgcentraltest -e 'insert into defaultDb (genome, name) values ("T. castaneum", "triCas2");'
    hgsql -N hgcentraltest -e 'insert into genomeClade (genome, clade, priority) values ("T. castaneum", "insect", "100");'
    cd ~/kent/src/hg/makeDb/trackDb
    cvs update
    # Edit trackDb/makefile to add triCas2 to the DBS variable.
    mkdir -p beetle/triCas2
    touch beetle/triCas2/description.html
    cvs add beetle/triCas2
    cvs add beetle/triCas2/description.html
    cvs ci -m "Added triCas2 (red flour beetle)." makefile
    cvs ci -m "Empty initial trackDb.ra and description.html for triCas2" beetle
    # in a clean, updated tree's kent/src/hg/makeDb/trackDb:
    make alpha

# FIX CHROMOSOME NAMES (DONE 10/22/2005 Andy)
    ssh hgwdev
    cd /cluster/data/triCas2
    for file in \
      beetle.masked.fa \
      downloads/beetle.fa \
      bed/rmsk/rmsk.out \
      bed/simpleRepeat/trf.bed; do            
        sed 's/ChLG1=X/ChLG1X/' $file > tmp; mv tmp $file
    done
    hgsql triCas2 -e 'drop table chromInfo'
    faToTwoBit beetle.masked.fa triCas2.2bit
    hgsql triCas2 < ~/kent/src/hg/lib/chromInfo.sql
    twoBitInfo triCas2.2bit /dev/stdout | 
        awk '{printf("%s\t%s\t/gbdb/triCas2/triCas2.2bit\n", $1, $2)}' > chrom.sizes
    echo "load data local infile 'chrom.sizes' into table chromInfo;" | hgsql triCas2          
    cd bed/rmsk/
    hgsql triCas2 -e 'drop table rmsk'
    hgLoadOut triCas2 rmsk.out
    hgsql triCas2 -e 'rename table rmsk_rmsk to rmsk'
    hgsql triCas2 -e 'drop index bin       on rmsk; \
                  drop index genoStart on rmsk; \
                  drop index genoEnd   on rmsk; \
                  create index bin       on rmsk (genoName(11), bin); \
                  create index genoStart on rmsk (genoName(11), genoStart); \
                  create index genoEnd   on rmsk (genoName(11), genoEnd);' 
    cd ../simpleRepeat/
    hgLoadBed -sqlTable=/cluster/home/aamp/kent/src/hg/lib/simpleRepeat.sql \
       triCas2 simpleRepeat trf.bed    

# MAKE GC5BASE WIGGLE TRACK (DONE 10/22/2005 Andy)
    ssh hgwdev
    mkdir /cluster/data/triCas2/bed/gc5Base
    cd /cluster/data/triCas2/bed/gc5Base
    hgGcPercent -wigOut -doGaps -file=stdout -win=5 -verbose=2 triCas2 \
       /cluster/data/triCas2 | wigEncode stdin gc5Base.wig gc5Base.wib
    mkdir /gbdb/triCas2/wib
    ln -s `pwd`/gc5Base.wib /gbdb/triCas2/wib
    hgLoadWiggle -pathPrefix=/gbdb/triCas2/wib triCas2 gc5Base gc5Base.wig

## MAKE DOWNLOADABLE FILES (DONE 10/22/2005 Andy)
    ssh hgwdev
    cd /cluster/data/triCas2
    mkdir zips
    zip -j zips/allOut.zip rmsk/rmsk.out
    zip -j zips/allFa.zip beetle.masked.fa
#    zip -j zips/allTrf.zip bed/simpleRepeat/trfMask.bed    
    zip -j zips/allAgp.zip downloads/beetle.agp
    ssh hgwdev
    mkdir -p /usr/local/apache/htdocs/goldenPath/triCas2
    cd /usr/local/apache/htdocs/goldenPath/triCas2
    mkdir bigZips database
    # Create README.txt files in bigZips/ and database/ to explain the files.
    cd bigZips/
    cp -p /cluster/data/triCas2/zips/*.zip .
    md5sum *.zip > md5sum.txt
    # check permissions
    chmod 664 *

# MAKE 11.OOC FILE FOR BLAT (DONE 10/22/2005 Andy)
    ssh hgwdev
    cd /cluster/data/triCas2
    blat triCas2.2bit /dev/null /dev/null -tileSize=11 -makeOoc=11.ooc -repMatch=300

# APIMEL2 BLASTZ (DONE 10/23/2005 Andy)
    ssh hgwdev
    cd /SAN
    mkdir blastz.apiMel2.2005-10-22
    ln -s blastz.apiMel2.2005-10-22 blastz.apiMel2
    cd blastz.apiMel2/
    cp /cluster/data/triCas2/{triCas2.2bit,chrom.sizes} .
    cat << "_EOF_" > DEF
# T. castaneum vs. A. mellifer

export PATH=/usr/bin:/bin:/usr/local/bin:/cluster/bin/penn:/cluster/bin/x86_64:/cluster/h
ome/angie/schwartzbin:/parasol/bin

BASE=/san/sanVol1/scratch/triCas2/blastz.apiMel2.2005-10-22

BLASTZ=blastz.v7.x86_64
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_Q=/san/sanVol1/scratch/triCas2/blastz.apiMel2.2005-10-22/HoxD55.q
BLASTZ_ABRIDGE_REPEATS=0

# TARGET - T. castaneum
SEQ1_DIR=$BASE/triCas2.2bit
SEQ1_CHUNK=5000000
SEQ1_LAP=10000
SEQ1_LEN=$BASE/chrom.sizes
SEQ1_LIMIT=30

# QUERY - A. mellifer
SEQ2_DIR=/scratch/hg/andy/apiMel2/nib
SEQ2_CHUNK=2000000000
SEQ2_LAP=0
SEQ2_LEN=/scratch/hg/andy/apiMel2/chrom.sizes

TMPDIR=/scratch/tmp
_EOF_
   doBlastzChainNet.sh -bigClusterHub pk -smallClusterHub pk DEF >& run.log &
   # monitor and continue where it breaks
   ./cleanUp.csh
   cd ../
   cp -r blastz.apiMel2.2005-10-22/ /cluster/data/triCas2/bed/

# DM2 BLASTZ (DONE 10/23/2005 Andy)
   ssh hgwdev
   cd /SAN
   mkdir blastz.dm2.2005-10-23
   cd blastz.dm2.2005-10-23/
   cp /cluster/data/triCas2/{triCas2.2bit,chrom.sizes} .
   cp -r /cluster/data/dm2/nib/ dm2.nib
   mv chrom.sizes triCas2.sizes
   cat << "_EOF_" > DEF
# T. castaneum vs. D. melanogaster

export PATH=/usr/bin:/bin:/usr/local/bin:/cluster/bin/penn:/cluster/bin/x86_64:/cluster/h
ome/angie/schwartzbin:/parasol/bin

BASE=/san/sanVol1/scratch/triCas2/blastz.dm2.2005-10-23

BLASTZ=blastz.v7.x86_64
BLASTZ_H=2000
BLASTZ_Y=3400
BLASTZ_L=4000
BLASTZ_K=2200
BLASTZ_Q=$BASE/HoxD55.q
BLASTZ_ABRIDGE_REPEATS=0

# TARGET - T. castaneum
SEQ1_DIR=$BASE/triCas2.2bit
SEQ1_CHUNK=2000000
SEQ1_LAP=10000
SEQ1_LEN=$BASE/triCas2.sizes
SEQ1_LIMIT=15

# QUERY - D. melanogaster
SEQ2_DIR=$BASE/dm2/nib
SEQ2_CHUNK=2000000000
SEQ2_LAP=0
SEQ2_LEN=$BASE/dm2.sizes

TMPDIR=/scratch/tmp
_EOF_
    screen
    doBlastzChainNet.pl -bigClusterHub pk -smallClusterHub pk DEF >& run.log &
    screen -d
    ## PROBLEMS!
    ## During the chainRun step, 24/171 failed 4 times
    # ssh pk
    # cd /SAN/blastz.dm2.2005-10-23/axtChain/run
    # para check
##171 jobs in batch
##37257 jobs (including everybody's) in Parasol queue.
##Checking finished jobs
##crashed: 24
##ranOk: 147
##failed 4 times: 24
##total jobs in batch: 171
    ## OK... this happens because the input in pslParts/ for these 24 jobs is
    ## all comments.  Double-check this:
    # for f in `cat problems`; do zcat ../../pslParts/$f.psl.gz | grep -v "^#"; done
    ## ... nothing.  OK no big deal, just pretend the chainRun.csh script finished
    ## and continue with chainMerge.

# MAKE HGCENTRALTEST BLATSERVERS ENTRY (DONE 12/12/2005 Andy)
    ssh hgwdev
    hgsql -N hgcentraltest -e 'insert into blatServers values("triCas2", "blat19", "17784", 1, 0);
          insert into blatServers values("triCas2", "blat19", "17784", 0, 1);'

# FLY PROTEINS TBLASTN (DONE 12/14/2005 Andy)
    ssh hgwdev
    cd san/triCas2/
    mkdir tblastn.dm2
    cd tblastn.dm2/

    # Download x64 NCBI Blast
    mkdir blast
    cd blast/
    wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/blast-2.2.13-x64-linux.tar.gz
    tar xfz blast-2.2.13-x64-linux.tar.gz 
    ln -s blast-2.2.13/{bin,data}
    cd ../

    # Make the blast database (target)
    ssh kkstore01
    cd /cluster/data/triCas2
    mkdir splits
    faSplit -oneFile -lift=splits/splits.lft size beetle.masked.fa 10000000 splits/splits    
    cd splits/
    faSplit sequence splits.fa 20 beet_
    rm splits.fa
    ssh kolossus
    cd san/triCas2/tblastn.dm2/splits/
    for fa in beet*.fa; do
       split=${fa%.fa}
       ../blast/bin/formatdb -i $fa -pF -n $split
    done
    rm *.fa formatdb.log 

    # Make queries 
    ssh hgwdev
    cd san/triCas2/tblastn.dm2/
    mkdir flyBaseExons
    cd flyBaseExons/
    # I want about 500 pieces
    calc `cat /cluster/data/dm2/bed/blat.dm2FB/dm2FB.psl | wc -l`/500
#18929/500 = 37.858000
    splitFile /cluster/data/dm2/bed/blat.dm2FB/dm2FB.psl 38 fbExons_
    for exonPsl in *; do pslxToFa $exonPsl $exonPsl.fa; rm $exonPsl; done

    # Set up run
    ssh pk
    cd san/triCas2/tblastn.dm2/
    ls -1S flyBaseExons/*.fa > exons.lst
    ls -1S splits/beet*.nsq > targets.lst
    cp /cluster/data/dm2/bed/blat.dm2FB/protein.lft .
    cp /san/sanVol1/scratch/andy/tblastnExons .
    mv splits/splits.lft .  
    mkdir blastOut/
    cat << "EOF" > blastGsub
#LOOP
./tblastnExons {check in exists $(path1)} {check in line $(path2)} {check out exists blastOut/$(root2)/q.$(root1).psl} splits.lft protein.lft ./blast/data ./blast/bin/blastall
#ENDLOOP
EOF
    chmod +x tblastnExons
    gensub2 targets.lst exons.lst blastGsub spec
    para create spec
    para try
    para push
    para time
#Completed: 9980 of 9980 jobs
#CPU time in finished jobs:     375481s    6258.02m   104.30h    4.35d  0.012 y
#IO & Wait Time:                 78520s    1308.66m    21.81h    0.91d  0.002 y
#Average job time:                  45s       0.76m     0.01h    0.00d
#Longest running job:                0s       0.00m     0.00h    0.00d
#Longest finished job:             478s       7.97m     0.13h    0.01d
#Submission to last job:          1413s      23.55m     0.39h    0.02d

    # Chaining part
    ssh kkstore01
    cd /cluster/data/triCas2/bed
    cp -r /san/sanVol1/scratch/triCas2/tblastn.dm2 .
    cd tblastn.dm2/blastOut/
    for dir in *; do 
      pushd $dir
      cat *.psl | simpleChain -prot -outPsl -maxGap=25000 /dev/stdin ../c.${dir}.psl
      popd
    done
    mkdir ../simpleChain
    mv *.psl ../simpleChain/
    cd ../simpleChain/
    for psl in *; do 
       part=${psl#c.}; part=${part%.psl}; echo $part
       awk "(\$13 - \$12)/\$11 > 0.6 {print}" c.$part.psl > c60.$part.psl
       sort -rn c60.$part.psl | pslUniq stdin u.$part.psl
       awk "((\$1 / \$11) ) > 0.60 { print   }" c60.$part.psl > m60.$part.psl
    done
    sort -u -T /tmp -k 14,14 -k 16,16n -k 17,17n u.*.psl m60* > ../blastnDm2.psl

    # Load
    ssh hgwdev
    cd /cluster/data/triCas2/bed/tblastn.dm2
    hgLoadPsl triCas2 blastDm2FB.psl

# HUMAN PROTEINS TBLASTN (Done 12/14/2005 Andy)
    ssh hgwdev
    cd san/triCas2/
    mkdir tblastn.hg17
    cd tblastn.hg17/
    ln -s ../../andy/triCas2.tblastn/splits.lft 
    ln -s ../../andy/triCas2.tblastn/splits
    ln -s ../../andy/blast
    mkdir humanKgExons
    cd humanKgExons/
    # I want about 1000 pieces
    calc `cat /cluster/data/hg17/bed/blat.hg17KG/hg17KG.psl | wc -l`/ 1000
#18929/500 = 37.365
    splitFile /cluster/data/hg17/bed/blat.hg17KG/hg17KG.psl 38 kgExons_
    for exonPsl in *; do pslxToFa $exonPsl $exonPsl.fa; rm $exonPsl; done

    # Begin run
    ssh pk
    cd san/triCas2/tblastn.hg17/
    ls -1S humanKgExons/*.fa > exons.lst
    ls -1S splits/beet*.nsq > targets.lst
    cp /cluster/data/hg17/bed/blat.hg17KG/protein.lft .
    cp /san/sanVol1/scratch/andy/tblastn{Exons,Gsub} .
    mkdir blastOut/
    gensub2 targets.lst exons.lst tblastnGsub spec
    para create spec
    para try
    para push
    para time
#Completed: 19680 of 19680 jobs
#CPU time in finished jobs:    1258626s   20977.10m   349.62h   14.57d  0.040 y
#IO & Wait Time:                 95442s    1590.70m    26.51h    1.10d  0.003 y
#Average job time:                  69s       1.15m     0.02h    0.00d
#Longest running job:                0s       0.00m     0.00h    0.00d
#Longest finished job:             410s       6.83m     0.11h    0.00d
#Submission to last job:          3891s      64.85m     1.08h    0.05d

    # Chaining
    ssh kkstore01
    cd /cluster/data/triCas2/bed
    cp -rd /san/sanVol1/scratch/triCas2/tblastn.hg17 .
    cd tblastn.hg17/blastOut/
    cp /san/sanVol1/scratch/andy/triCas2.tblastn/tblastnChain ../
    ../tblastnChain blastHg17KG.psl
    
    # Loading
    ssh hgwdev
    cd /cluster/data/triCas2/bed/tblastn.hg17
    hgLoadPsl triCas2 blastHg17KG.psl


###########################################################################
# FIX UP AGP, RELOAD GOLD (DONE 10/26/06 angie)
    # The AGP contains a bunch of "ChLG1=X" lines but the sequence name 
    # is "ChLG1X" -- fix it, reload, and leave the fixed .agp file in a 
    # place where makeDownloads.pl will find it.
    ssh hgwdev
    cd /cluster/data/triCas2
    sed -e 's/ChLG1=X/ChLG1X/' downloads/nocomments.agp > triCas2.agp
    hgGoldGapGl -noGl triCas2 triCas2.agp


###########################################################################
# REPLACE trfMask.bed (DONE 10/26/06 angie)
    # I see trfMask.bed mentioned earlier in the file, but it is no longer
    # anywhere under /cluster/data/triCas2.  Regenerating:
    cd /cluster/data/triCas2/bed/simpleRepeat
    awk '{if ($5 <= 12) print;}' trf.bed > trfMask.bed


###########################################################################
# MAKE DOWNLOADABLE FILES (DONE 10/26/06 angie)
    ssh kkstore04
    makeDownloads.pl triCas2
    # Edit README.txt files as directed by script output (add link to 
    # Baylor's project page and RepeatMasker version info).