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

# This file describes browser build for the galVar1
# Malayan flying lemur - Galeopterus variegatus

# Assembly Name:  G_variegatus-3.0.2
# Organism name:  Galeopterus variegatus
# Taxid:          482537
# Submitter:      Washington University (WashU)
# Date:           2014-6-5
# BioSample:      SAMN01758971
# Assembly type:  haploid
# Release type:   major
# Assembly level: Scaffold
# Genome representation: full
# GenBank Assembly Accession: GCA_000696425.1 (latest)
# RefSeq Assembly Accession: GCF_000696425.1 (species-representative latest)
# RefSeq Assembly and GenBank Assemblies Identical: no
#
## Assembly-Units:
## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
## GCA_000696435.1      GCF_000696435.1 Primary Assembly
##      GCF_000037935.1 non-nuclear

#############################################################################
# fetch sequence from new style download directory (DONE - 2016-02-26 - Hiram)
    mkdir -p /hive/data/genomes/galVar1/refseq
    cd /hive/data/genomes/galVar1/refseq

export asmName="GCF_000696425.1_G_variegatus-3.0.2"
export asmType="refseq"
export D="vertebrate_mammalian/Galeopterus_variegatus/all_assembly_versions/$asmName"

time rsync -a -P -L \
   rsync://ftp.ncbi.nlm.nih.gov/genomes/${asmType}/${D}/ ./
# sent 486 bytes  received 3281060733 bytes  11952864.19 bytes/sec
# total size is 3280657709  speedup is 1.00
# real    4m34.536s

    # measure what we have here:
    faSize *genomic.fna.gz
# 3187660572 bases (384823142 N's 2802837430 real 1899580299 upper 903257131 lower) in 179514 sequences in 1 files
# Total size: mean 17757.2 sd 77110.0 min 309 (NW_007753091.1) max 3276566 (NW_007726111.1) median 913
# %28.34 masked total, %32.23 masked real

    # check for duplicate sequences:

    mkdir /hive/data/genomes/galVar1/ucsc
    cd /hive/data/genomes/galVar1/ucsc
    faToTwoBit ../refseq/*_genomic.fna.gz refseq.2bit
    twoBitDup refseq.2bit
    # no output is a good result
    rm refseq.2bit

#############################################################################
# fixup to UCSC naming scheme (DONE - 2016-03-01 - Hiram)
    mkdir /hive/data/genomes/galVar1/ucsc
    cd /hive/data/genomes/galVar1/ucsc

    # since this is a scaffold-only assembly, merely use the accession names
    # and since there are all .1 versions, this sed statement will make them
    # all v1 version names:
    zcat ../refseq/GCF_000696425.1_G_variegatus-3.0.2_assembly_structure/Primary_Assembly/unplaced_scaffolds/AGP/unplaced.scaf.agp.gz \
       | grep -v "^#" | sed -e 's/\.1/v1/;' > chrUn.galVar1.agp

    zcat ../refseq/GCF_000696425.1_G_variegatus-3.0.2_assembly_structure/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fna.gz \
       | sed -e 's/.1 Galeopterus .*/v1/;' > chrUn.galVar1.fa

    zcat ../refseq/GCF_000696425.1_G_variegatus-3.0.2_assembly_structure/non-nuclear/assembled_chromosomes/FASTA/chrMT.fna.gz \
      | sed -e 's/>NC_004031.1 G.*/>chrM/;' > chrM.fa

    zcat ../refseq/GCF_000696425.1_G_variegatus-3.0.2_assembly_structure/non-nuclear/assembled_chromosomes/AGP/chrMT.comp.agp.gz \
      | grep -v "^#" |  sed -e 's/NC_004031.1/chrM/;' > chrM.agp

    # verify these fasta and agp files are correct:
    faToTwoBit *.fa t.2bit
    cat chr*.agp | checkAgpAndFa stdin t.2bit 2>&1 | tail
    # All AGP and FASTA entries agree - both files are valid

    # verify nothing lost compared to genbank:
    faSize *.fa
# 3187660572 bases (384823142 N's 2802837430 real 2802837430 upper 0 lower)
#    in 179514 sequences in 2 files
# Total size: mean 17757.2 sd 77110.0 min 309 (NW_007753091v1)
#    max 3276566 (NW_007726111v1) median 913

    # same totals as above: (except for masking)
# 3187660572 bases (384823142 N's 2802837430 real 1899580299 upper 903257131 lower)
#    in 179514 sequences in 1 files
# Total size: mean 17757.2 sd 77110.0 min 309 (NW_007753091.1)
#    max 3276566 (NW_007726111.1) median 913

#############################################################################
#  Initial database build (DONE - 2016-01-29 - Hiram)

    cd /hive/data/genomes/galVar1
    printf "%s" '# Config parameters for makeGenomeDb.pl:
db galVar1
clade mammal
genomeCladePriority 35
scientificName Galeopterus variegatus
commonName Malayan flying lemur
assemblyDate Jun. 2014
assemblyLabel Washington University (WashU)
assemblyShortLabel G_variegatus-3.0.2
orderKey 13060
# chrM included in the refseq sequence assembly
#  mitoAcc NC_004031.1
mitoAcc none
fastaFiles /hive/data/genomes/galVar1/ucsc/chr*.fa
agpFiles /hive/data/genomes/galVar1/ucsc/chr*.agp
# qualFiles none
dbDbSpeciesDir galVar
photoCreditURL https://www.flickr.com/photos/64565252@N00/453554996
# https://upload.wikimedia.org/wikipedia/commons/c/cd/Colugo_%28Galeopterus_variegatus%2C_adult_female%29%2C_Central_Catchment_Area%2C_Singapore_-_20060618.jpg
photoCreditName Lip Kee Yap
ncbiGenomeId 792
ncbiAssemblyId 182621
ncbiAssemblyName G_variegatus-3.0.2
ncbiBioProject 253111
genBankAccessionID GCF_000696425.1
taxId 482537
' > galVar1.config.ra

    # verify sequence and AGP are OK:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev -fileServer=hgwdev \
         -stop=agp galVar1.config.ra) > agp.log 2>&1
    # *** All done!  (through the 'agp' step)
    # real    3m45.436s

    # then finish it off:
    time (makeGenomeDb.pl -workhorse=hgwdev -dbHost=hgwdev \
       -fileServer=hgwdev -continue=db galVar1.config.ra) > db.log 2>&1
    # real    26m21.384s

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

#########################################################################
# ucscToINSDC table/track (DONE - 2016-04-14 - Hiram)
    # the sequence here is working for a 'refseq' assembly with a chrM
    # situation may be specific depending upon what is available in the assembly

    mkdir /hive/data/genomes/galVar1/bed/ucscToINSDC
    cd /hive/data/genomes/galVar1/bed/ucscToINSDC

    # find accession for chrM
    grep chrM ../../galVar1.agp
# chrM    1       16748   1       O       NC_004031.1     1       16748   +

    # use that accession here:
    ~/kent/src/hg/utils/automation/ucscToINSDC.sh \
        ../../refseq/GCF_*structure/Primary_Assembly NC_004031.1
    awk '{printf "%s\t%s\n", $2, $1}' ucscToINSDC.txt | sort > insdcToUcsc.txt
    # there is no name for chrM/NC_001323.1 sequence, there is no such
    #  sequence with an INSDC name
    grep -v "^#" ../../refseq/GCF*_assembly_report.txt | cut -f5,7 \
      | sed -e 's/na\b/notAvailable/;' | awk '{printf "%s\t%s\n", $2, $1}' \
         | sort > insdc.refseq.txt
    # the sed \b means to match word

    awk '{printf "%s\t0\t%d\n", $1,$2}' ../../chrom.sizes \
         | sort > name.coordinate.tab
    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 *
    # 179514 insdc.refseq.txt
    # 179514 insdcToUcsc.txt
    # 179514 name.coordinate.tab
    # 179514 ucscToINSDC.bed
    # 179514 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 galVar1 ucscToINSDC stdin ucscToINSDC.bed
    checkTableCoords galVar1
    # should cover %100 entirely:
    featureBits -countGaps galVar1 ucscToINSDC
    # 3187660572 bases of 3187660572 (100.000%) in intersection

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2016-03-01 - Hiram)
    hgsql -N -e "select frag from gold;" galVar1 | sort | head -1
JMZW01000001.1

    hgsql -N -e "select frag from gold;" galVar1 | sort | tail -2
JMZW01511877.1
NC_004031.1

[AN][MC][Z_][W0][0-9]+(\.[0-9]+)?
    # verify this rule will find them all or eliminate them all:
    hgsql -N -e "select frag from gold;" galVar1 | wc -l
    # 511878

    hgsql -N -e "select frag from gold;" galVar1 \
       | egrep -e '[JN][MC][Z_][W0]0[0-9]+(\.[0-9]+)?' | wc -l
    # 511878

    hgsql -N -e "select frag from gold;" galVar1 \
       | egrep -v -e '[JN][MC][Z_][W0]0[0-9]+(\.[0-9]+)?' | wc -l
    # 0

    # hence, add to trackDb/rhesus/galVar1/trackDb.ra
searchTable gold
shortCircuit 1
termRegex [JN][MC][Z_][W0]0[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 - 2016-03-01 - Hiram)
    mkdir /hive/data/genomes/galVar1/bed/repeatMasker
    cd /hive/data/genomes/galVar1/bed/repeatMasker
    time  (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku galVar1) > do.log 2>&1
    # real    920m31.663s

    cat faSize.rmsk.txt
# 3187660572 bases (384823142 N's 2802837430 real 1720575153 upper
#    1082262277 lower) in 179514 sequences in 1 files
# Total size: mean 17757.2 sd 77110.0 min 309 (NW_007753091v1)
#    max 3276566 (NW_007726111v1) median 913
# %33.95 masked total, %38.61 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 galVar1 rmsk
    # 1082721915 bases of 3187660572 (33.966%) in intersection
    # real    1m55.351s

    # 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

    # faster way to get the same result:
    time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' galVar1 \
        | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total"
    # total 1082721915.000000
    # real    0m36.946s

##########################################################################
# running simple repeat (DONE - 2016-03-01 - Hiram)

    mkdir /hive/data/genomes/galVar1/bed/simpleRepeat
    cd /hive/data/genomes/galVar1/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        galVar1) > do.log 2>&1
    # real    109m31.431s

    cat fb.simpleRepeat
    # 106068577 bases of 2802917674 (3.784%) in intersection

    # add to rmsk after it is done:
    cd /hive/data/genomes/galVar1
    twoBitMask galVar1.rmsk.2bit \
        -add bed/simpleRepeat/trfMask.bed galVar1.2bit
    #   you can safely ignore the warning about fields >= 13
    twoBitToFa galVar1.2bit stdout | faSize stdin > faSize.galVar1.2bit.txt
    cat faSize.galVar1.2bit.txt
# 3187660572 bases (384823142 N's 2802837430 real 1719181078 upper
#    1083656352 lower) in 179514 sequences in 1 files
# Total size: mean 17757.2 sd 77110.0 min 309 (NW_007753091v1)
#    max 3276566 (NW_007726111v1) median 913
# %34.00 masked total, %38.66 masked real

    rm /gbdb/galVar1/galVar1.2bit
    ln -s `pwd`/galVar1.2bit /gbdb/galVar1/galVar1.2bit

#########################################################################
# CREATE MICROSAT TRACK (DONE - 2016-03-04 - Hiram)
    ssh hgwdev
    mkdir /cluster/data/galVar1/bed/microsat
    cd /cluster/data/galVar1/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 galVar1 microsat microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2016-03-04 - Hiram)

    mkdir /hive/data/genomes/galVar1/bed/windowMasker
    cd /hive/data/genomes/galVar1/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev galVar1) > do.log 2>&1
    # real    639m26.741s

    # Masking statistics
    cat faSize.galVar1.cleanWMSdust.txt
# 3187660572 bases (384823142 N's 2802837430 real 1884079862 upper
#    918757568 lower) in 179514 sequences in 1 files
# Total size: mean 17757.2 sd 77110.0 min 309 (NW_007753091v1)
#    max 3276566 (NW_007726111v1) median 913
# %28.82 masked total, %32.78 masked real

    cat fb.galVar1.rmsk.windowmaskerSdust.txt
    # 493373693 bases of 3187660572 (15.478%) in intersection

##########################################################################
# cpgIslands - (DONE - 2016-03-07 - Hiram)
    mkdir /hive/data/genomes/galVar1/bed/cpgIslands
    cd /hive/data/genomes/galVar1/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku galVar1) > do.log 2>&1
    # real    21m45.475s

    cat fb.galVar1.cpgIslandExt.txt
    # 30462018 bases of 2802917674 (1.087%) in intersection

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2016-03-01 - Hiram)
    mkdir /hive/data/genomes/galVar1/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/galVar1/bed/cpgIslandsUnmasked

    # run stepwise so the loading can be done in a different table
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/galVar1/galVar1.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku galVar1) > do.log 2>&1
    # real    43m23.093s

    cat fb.galVar1.cpgIslandExtUnmasked.txt
    # 33579201 bases of 2802917674 (1.198%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2016-03-01 - Hiram)
    mkdir /hive/data/genomes/galVar1/bed/cytoBand
    cd /hive/data/genomes/galVar1/bed/cytoBand
    makeCytoBandIdeo.csh galVar1

#########################################################################
# genscan - (DONE - 2016-03-07 - Hiram)
    mkdir /hive/data/genomes/galVar1/bed/genscan
    cd /hive/data/genomes/galVar1/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku galVar1) > do.log 2>&1
    # real    92m41.897s

    cat fb.galVar1.genscan.txt
    # 66144712 bases of 2802917674 (2.360%) in intersection

    cat fb.galVar1.genscanSubopt.txt
    # 75687535 bases of 2802917674 (2.700%) in intersection

#############################################################################
# augustus gene track (DONE - 2016-03-07 - Hiram)

    mkdir /hive/data/genomes/galVar1/bed/augustus
    cd /hive/data/genomes/galVar1/bed/augustus
    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
        -species=human -dbHost=hgwdev \
           -workhorse=hgwdev galVar1) > do.log 2>&1
    # real    88m28.161s

    cat fb.galVar1.augustusGene.txt
    # 66133815 bases of 2802917674 (2.359%) in intersection

##########################################################################
#  BLATSERVERS ENTRY (DONE - 2016-04-14 - 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 ("galVar1", "blat1a", "17860", "1", "0"); \
	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("galVar1", "blat1a", "17861", "0", "1");' \
	    hgcentraltest
    #	test it with some sequence

############################################################################
# Create kluster run files (DONE - 2016-03-07 - Hiram)

    # numerator is galVar1 gapless bases "real" as reported by:
    featureBits -noRandom -noHap galVar1 gap
    # 384742898 bases of 2802917674 (13.727%) 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 \( 2802917674 / 2861349177 \) \* 1024
    #  ( 2802917674 / 2861349177 ) * 1024 = 1003.088935

    # ==> use -repMatch=1000 according to size scaled down from 1024 for human.
    #   and rounded down to nearest 50
    cd /hive/data/genomes/galVar1
    blat galVar1.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/galVar1.11.ooc \
        -repMatch=1000
    #   Wrote 26641 overused 11-mers to jkStuff/galVar1.11.ooc

    #   there are no non-bridged gaps, no need to run up this liftUp file:
#     hgsql -N \
#         -e 'select * from gap where bridge="no" order by size;' galVar1 \
#         | 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 galVar1 jkStuff/nonBridged.lft \
#         -bedFile=jkStuff/nonBridged.bed

########################################################################
# GENBANK AUTO UPDATE (DONE - 2016-03-08 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism       mrnaCnt estCnt  refSeqCnt
    # Galeopterus variegatus
    # there is no entry for this species in the organism.lst file

    # edit etc/genbank.conf to add galVar1 just before micMur2

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

    git commit -m "Added galVar1 - Galeopterus variegatus - Malayan flying lemur ; no redmine" 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 galVar1 Galeopterus variegatus - Malayan flying lemur no redmine" \
       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 galVar1
    # logFile: var/build/logs/2016.03.07-12:33:47.galVar1.initalign.log
    #   real    843m10.492s

    #   To re-do, rm the dir first:
    #     /cluster/data/genbank/work/initial.galVar1

    # load database when finished
    ssh hgwdev
    cd /cluster/data/genbank
    time ./bin/gbDbLoadStep -drop -initialLoad galVar1
    # logFile: var/dbload/hgwdev/logs/2016.03.08-09:51:06.galVar1.dbload.log
    #  real    58m6.227s


    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add galVar1 to:
    #   etc/align.dbs etc/hgwdev.dbs
    git add etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added galVar1 - Galeopterus variegatus/Malayan flying lemur refs #17180" etc/align.dbs etc/hgwdev.dbs

    git push
    make etc-update

############################################################################
## reset default position to GULO gene (Vitamin C)
##  (DONE - 2016-05-18 - Hiram)

    ssh hgwdev
    hgsql -e 'update dbDb set defaultPos="NW_007732982v1:59339-77043"
	where name="galVar1";' hgcentraltest

#############################################################################
# all.joiner update, downloads and in pushQ - (DONE - 2016-04-14 - Hiram)
    cd $HOME/kent/src/hg/makeDb/schema
    # fixup all.joiner until this is a clean output
    joinerCheck -database=galVar1 -tableCoverage all.joiner
    joinerCheck -database=galVar1 -times all.joiner
    joinerCheck -database=galVar1 -keys all.joiner
    git commit -m 'adding rules for galVar1 refs #17180' all.joiner
    git push

    cd /hive/data/genomes/galVar1
    time (makeDownloads.pl galVar1) > downloads.log 2>&1
    #  real    19m37.483s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/galVar1/pushQ
    cd /hive/data/genomes/galVar1/pushQ
    time makePushQSql.pl galVar1 > galVar1.pushQ.sql 2> stderr.out
    #  real    5m46.564s

    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: hgwdev does not have /gbdb/galVar1/wib/gc5Base.wib
    # WARNING: hgwdev does not have /gbdb/galVar1/wib/quality.wib
    # WARNING: hgwdev does not have /gbdb/galVar1/bbi/quality.bw
    # WARNING: galVar1 does not have seq
    # WARNING: galVar1 does not have extFile

    #   copy it to hgwbeta
    scp -p galVar1.pushQ.sql qateam@hgwbeta:/tmp/
    ssh qateam@hgwbeta "./bin/x86_64/hgsql qapushq < /tmp/galVar1.pushQ.sql"

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

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