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

# This file describes browser build for the regenRn0

#  Can use existing photograph (otherwise find one before starting here)

#########################################################################
#  Initial steps, use existing photograph (DONE - 2019-06-28 - Hiram)

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

mkdir ~/kent/src/hg/makeDb/doc/regenRn0
cd ~/kent/src/hg/makeDb/doc/regenRn0

sed -e 's/galGal6/regenRn0/g; s/GalGal6/RegenRn0/g; s/DONE/TBD/g;' \
	../galGal6/initialBuild.txt > initialBuild.txt

mkdir -p /hive/data/genomes/regenRn0/regeneron
# sequences were obtained via email instructions from Regeneron
# downloaded from a URl for their secure situation
# -rw-rw-r-- 1    1149864 Jan 31 12:12 EXP_REFINEFINAL1_bppAdjust_cmap_REGN_DA_Rat_Assembly_fasta_NGScontigs_HYBRID_SCAFFOLD.agp
# -rw-rw-r-- 1 2762579559 May  3 11:39 REGN_DA_Rat_HybridScaffold_ALL.fasta
# -rw-rw-r-- 1  691843031 May  3 11:52 REGN_DA_Rat_HybridScaffold_ALL.2bit

#  Can use existing photograph
cp -p ../rn6/photoReference.txt .
cat photoReference.txt
photoCreditURL  http://www.genome.gov/dmd/img.cfm?node=Photos/Animals/Rat%20(brown%20norway)&id=79111
photoCreditName NHGRI press photos

# check assembly size for later reference:

faSize REGN_DA*.fasta
# 2762435742 bases (227617579 N's 2534818163 real 2513670233 upper
#	21147930 lower) in 7100 sequences in 1 files
# Total size: mean 389075.5 sd 6359718.0 min 1 (012480F_pilon_obj)
#	max 248247500 (Super-Scaffold_100001) median 10145
# %0.77 masked total, %0.83 masked real

# verify the 2bit file is the same
twoBitToFa REGN_DA_Rat_HybridScaffold_ALL.2bit stdout | faSize stdin
# 2762435742 bases (227617579 N's 2534818163 real 2513670233 upper
#	21147930 lower) in 7100 sequences in 1 files
# Total size: mean 389075.5 sd 6359718.0 min 1 (012480F_pilon_obj)
#	max 248247500 (Super-Scaffold_100001) median 10145
# %0.77 masked total, %0.83 masked real

# these tiny duplicates will be eliminated later during the size
# cut-off filter::
twoBitDup REGN_DA_Rat_HybridScaffold_ALL.2bit
# 012415F_pilon_obj and 012413F_pilon_obj are identical
# 012425F_pilon_obj and 012424F_pilon_obj are identical
# 012419F_pilon_obj and 012420F_pilon_obj are identical

#############################################################################
# establish config.ra file (DONE - Hiram - 2019-06-28)
    cd /hive/data/genomes/regenRn0
    # copy the rn6 file and edit:

    cat regenRn9.config.ra
# Config parameters for makeGenomeDb.pl:
db regenRn0
clade mammal
scientificName Rattus norvegicus
commonName Rat
assemblyDate May. 2019
assemblyLabel Regeneron rat
assemblyShortLabel Regen Rn0
orderKey 18021
mitoAcc none
fastaFiles /hive/data/genomes/regenRn0/ucsc/ucsc.fa.gz
agpFiles /hive/data/genomes/regenRn0/ucsc/fake.agp
# qualFiles none
dbDbSpeciesDir rat
photoCreditURL http://www.genome.gov/10005141
photoCreditName NHGRI Press Photos
ncbiGenomeId 73
ncbiAssemblyId 382928
ncbiAssemblyName RegenRn0
ncbiBioProject 10629
ncbiBioSample SAMN02808228
genBankAccessionID GCA_000001895.4
taxId 10116

    # compare with previous version to see if it is sane:
    diff regenRn0.config.ra ../rn6/rn6.config.ra

#############################################################################
# setup UCSC named files (DONE - 2019-06-28 - Hiram)

    mkdir /hive/data/genomes/regenRn0/ucsc
    cd /hive/data/genomes/regenRn0/ucsc

    # limit to contigs only 100 bases and larger:

    awk '$2 > 99' ../regeneron/REGN_DA_Rat_HybridScaffold_ALL.chrom.sizes \
  > limit.sizes

    cut -f1 limit.sizes | sort > allowed.names

    # running this script to get the contig names shorter
    # result of this script output into: ucsc.regeneron.name.translate

#!/usr/bin/env perl

use strict;
use warnings;

open (FH, "<allowed.names") or die "can not read allowed.names";
while (my $line = <FH>) {
  chomp $line;
  my $ucscName = $line;
  if ($ucscName =~ m/^Super-Scaffold/) {
     $ucscName =~ s/Super-Scaffold_/ss/;
  } elsif ($ucscName =~ m/_pilon_obj$/) {
     $ucscName =~ s/_pilon_obj//;
     $ucscName =~ s/^/pi/;
  } elsif ($ucscName =~ m/pilon_subseq/) {
    if ($ucscName =~ m/000052F_pilon_subseq/) {
       $ucscName =~ s/32403:237079_obj//;
       $ucscName =~ s/027473:1032013_obj//;
       $ucscName =~ s/_pilon_subseq//;
    } else {
       $ucscName =~ s/_pilon_subseq_.*//;
    }
    $ucscName =~ s/^/pisub/;
  } else {
    die "can not recognize $ucscName";
  }
  printf "%s\t%s\n", $ucscName, $line;
}
close (FH);

    # did try to use the supplied AGP file, but it had trouble
    # it did not declare most of the gaps, and appears to declare gaps
    # that are not gaps.

    # this script translated the AGP file contig names:

#!/usr/bin/env perl

use strict;
use warnings;

my %regenToUcsc;        # key is Regeneron name, value is UCSC name

open (FH, "<ucsc.regeneron.name.translate") or die "can not read ucsc.regeneron.name.translate";
while (my $line = <FH>) {
   chomp $line;
   my ($ucsc, $regen) = split('\s+', $line);
   die "regen name already seen $regen" if (defined($regenToUcsc{$regen}));
   $regenToUcsc{$regen} = $ucsc;
}
close (FH);

open (FH, "<../regeneron/EXP_REFINEFINAL1_bppAdjust_cmap_REGN_DA_Rat_Assembly_fasta_NGScontigs_HYBRID_SCAFFOLD.agp") or die "can not read the agp file";
while (my $line = <FH>) {
  chomp $line;
  if ($line =~ m/^#/) {
    printf "%s\n", $line;
  } else {
    my @a = split('\s+', $line);
    if (defined($regenToUcsc{$a[0]})) {
      my $priName = $regenToUcsc{$a[0]};
      if ($a[6] =~ m/scaffold/) {
        shift @a;
        printf "%s\t%s\n", $priName, join("\t",@a);
      } else {
        my $ctgName = $a[5];
        $ctgName = $regenToUcsc{$a[5]} if (defined($regenToUcsc{$a[5]}));
        printf "%s\t%s\t%s\t%s\n", $priName, join("\t",@a[1..4]), $ctgName, join("\t",@a[6..8]);
      }
    } else {
      next;
    }
  }
}
close (FH);

    # this script translated the contig names in the fasta file
    # result into: | gzip -c > ucsc.fa.gz

#!/usr/bin/env perl

use strict;
use warnings;

my %regenToUcsc;        # key is Regeneron name, value is UCSC name

open (FH, "<ucsc.regeneron.name.translate") or die "can not read ucsc.regeneron.name.translate";
while (my $line = <FH>) {
   chomp $line;
   my ($ucsc, $regen) = split('\s+', $line);
   die "regen name already seen $regen" if (defined($regenToUcsc{$regen}));
   $regenToUcsc{$regen} = $ucsc;
}
close (FH);

my $skipping = 0;

open (FH, "<../regeneron/REGN_DA_Rat_HybridScaffold_ALL.fasta") or die "can not read the fasta file";
while (my $line = <FH>) {
  chomp $line;
  if ($line =~ m/^>/) {
    $line =~ s/>//;
    if (!defined($regenToUcsc{$line})) {
      $skipping = 1;
    } else {
      printf ">%s\n", $regenToUcsc{$line};
      $skipping = 0;
    }
  } else {
    if ($skipping) {
      next;
    } else {
      printf "%s\n", $line;
    }
  }
}
close (FH);


    # verify the resulting fasta is sane, and no duplicates:

    faToTwoBit ucsc.fa.gz test.2bit
    twoBitDup test.2bit
    # no output is a good result, otherwise, would have to eliminate duplicates
    # the scripts creating the fasta here will be using this refseq.2bit file
    # remove it later

    hgFakeAgp ucsc.fa.gz fake.agp
    checkAgpAndFa fake.agp test.2bit 2>&1 | tail -4
    # All AGP and FASTA entries agree - both files are valid

    twoBitToFa test.2bit stdout | faSize stdin
# 2762428432 bases (227617579 N's 2534810853 real 2513669505 upper
#	21141348 lower) in 6846 sequences in 1 files
# Total size: mean 403509.8 sd 6476189.8 min 101 (pi012238F)
#	max 248247500 (ss100001) median 10668
# %0.77 masked total, %0.83 masked real

    # no longer need the temporary 2bit file
    rm test.2bit

#############################################################################
#  Initial database build (DONE - 2019-06-28 - Hiram)

    # verify sequence and AGP are OK:
    time (makeGenomeDb.pl -stop=db regenRn0.config.ra -workhorse=hgwdev) \
       > db.log 2>&1
    # real    16m37.962s

    # finish it off:
    time (makeGenomeDb.pl -continue=dbDb regenRn0.config.ra -workhorse=hgwdev) \
	> dbDb.log 2>&1
    # real    0m6.469s

    # check in the trackDb files created in TemporaryTrackDbCheckout/
    #    and add regenRn0 to trackDb/makefile

    # temporary symlink until masked sequence is available
    cd /hive/data/genomes/regenRn0
    ln -s `pwd`/regenRn0.unmasked.2bit /gbdb/regenRn0/regenRn0.2bit

##############################################################################
# cpgIslands on UNMASKED sequence (DONE - 2019-06-28 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/cpgIslandsUnmasked
    cd /hive/data/genomes/regenRn0/bed/cpgIslandsUnmasked

    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku -buildDir=`pwd` \
       -tableName=cpgIslandExtUnmasked \
          -maskedSeq=/hive/data/genomes/regenRn0/regenRn0.unmasked.2bit \
             -workhorse=hgwdev -smallClusterHub=ku regenRn0) > do.log 2>&1
    # real    3m46.939s

    cat fb.regenRn0.cpgIslandExtUnmasked.txt
    # 11929440 bases of 2534810853 (0.471%) in intersection

#############################################################################
# cytoBandIdeo - (DONE - 2019-06-28 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/cytoBand
    cd /hive/data/genomes/regenRn0/bed/cytoBand
    makeCytoBandIdeo.csh regenRn0

#############################################################################
# run up idKeys files for chromAlias/ncbiRefSeq (TBD - 2019-06-28 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/idKeys
    cd /hive/data/genomes/regenRn0/bed/idKeys

    time (doIdKeys.pl \
        -twoBit=/hive/data/genomes/regenRn0/regenRn0.unmasked.2bit \
        -buildDir=`pwd` regenRn0) > do.log 2>&1 &
    # real    0m47.105s

    cat regenRn0.keySignature.txt
    #  7850e2d5dabb6134fdc9d7083f1a3a54

#############################################################################
# gapOverlap (DONE - 2019-06-28 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/gapOverlap
    cd /hive/data/genomes/regenRn0/bed/gapOverlap
    time (doGapOverlap.pl \
        -twoBit=/hive/data/genomes/regenRn0/regenRn0.unmasked.2bit regenRn0 ) \
        > do.log 2>&1 &
    # real    1m51.246s

    # there are 7 items found:
    wc -l bed.tab
    # 7 bed.tab

    cat fb.regenRn0.gapOverlap.txt
    # 5912 bases of 2762428432 (0.000%) in intersection

#############################################################################
# tandemDups (DONE - 2019-06-28 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/tandemDups
    cd /hive/data/genomes/regenRn0/bed/tandemDups
    time (~/kent/src/hg/utils/automation/doTandemDup.pl \
  -twoBit=/hive/data/genomes/regenRn0/regenRn0.unmasked.2bit regenRn0) \
        > do.log 2>&1 &
    # real    369m58.055s

    cat fb.regenRn0.tandemDups.txt
    # 86298981 bases of 2762428432 (3.124%) in intersection

    bigBedInfo regenRn0.tandemDups.bb | sed -e 's/^/#  /;'
#  version: 4
#  fieldCount: 13
#  hasHeaderExtension: yes
#  isCompressed: yes
#  isSwapped: 0
#  extraIndexCount: 0
#  itemCount: 1,039,087
#  primaryDataSize: 27,356,255
#  primaryIndexSize: 178,160
#  zoomLevels: 9
#  chromCount: 3504
#  basesCovered: 1,365,621,612
#  meanDepth (of bases covered): 6.439341
#  minDepth: 1.000000
#  maxDepth: 307.000000
#  std of depth: 12.663540

#########################################################################
# ucscToINSDC and ucscToRefSeq table/track (TBD - 2019-06-28 - Hiram)
    # construct idKeys for the refseq sequence
    mkdir /hive/data/genomes/regenRn0/refseq/idKeys
    cd /hive/data/genomes/regenRn0/refseq/idKeys
    faToTwoBit ../GCF_000002315.5_GRCg6a_genomic.fna.gz regenRn0.refSeq.2bit

    time (doIdKeys.pl -buildDir=`pwd` \
        -twoBit=`pwd`/regenRn0.refSeq.2bit refseqRegenRn0)  > do.log 2>&1 &
    # real    0m48.786s

    cat refseqRegenRn0.keySignature.txt
    #  7850e2d5dabb6134fdc9d7083f1a3a54

    # and the genbank sequence needs keys too:
    mkdir /hive/data/genomes/regenRn0/refseq/idKeysGenbank
    cd /hive/data/genomes/regenRn0/refseq/idKeysGenbank
    faToTwoBit /hive/data/outside/ncbi/genomes/genbank/vertebrate_other/Gallus_gallus/all_assembly_versions/GCA_000002315.5_GRCg6a/GCA_000002315.5_GRCg6a_genomic.fna.gz regenRn0.genbank.2bit

    time (doIdKeys.pl -buildDir=`pwd` \
        -twoBit=`pwd`/regenRn0.genbank.2bit genbankRegenRn0)  > do.log 2>&1 &

    cat genbankRegenRn0.keySignature.txt
    #  a20fdad3318d371fcb34fcc66bab3752

    mkdir /hive/data/genomes/regenRn0/bed/chromAlias

    join -t$'\t' ../idKeys/regenRn0.idKeys.txt \
        ../../refseq/idKeysGenbank/genbankRegenRn0.idKeys.txt | cut -f2- \
          | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \
            | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \
               | sort -k1,1 -k2,2n > ucscToINSDC.bed

    join -t$'\t' ../idKeys/regenRn0.idKeys.txt \
        ../../refseq/idKeys/refseqRegenRn0.idKeys.txt | cut -f2- \
          | sort -k1,1 | join -t$'\t' <(sort -k1,1 ../../chrom.sizes) - \
            | awk '{printf "%s\t0\t%d\t%s\n", $1, $2, $3}' \
               | sort -k1,1 -k2,2n > ucscToRefSeq.bed

    # should be same line counts throughout:
    wc -l * ../../chrom.sizes
    #	463 ucscToINSDC.bed
    #	464 ucscToRefSeq.bed
    #	464 ../../chrom.sizes

    # need to find the accession for the INSDC equivalent to chrM:
    egrep chrM *
# ucscToRefSeq.bed:chrM   0       16775   NC_001323.1
    # lookup that accession at NCBI Entrez: X52392.1
    # and add to ucscToINSDC.bed:
    printf "chrM\t0\t16775\tX52392.1\n" >> ucscToINSDC.bed
    # verify:
    grep chrM *
# ucsc.genbank.tab:chrM   X52392.1
# ucsc.refseq.tab:chrM    NC_001323.1
# ucscToINSDC.bed:chrM    0       16775   X52392.1
# ucscToRefSeq.bed:chrM   0       16775   NC_001323.1

    export chrSize=`cut -f1 ucscToINSDC.bed | awk '{print length($0)}' | sort -n | tail -1`
    echo $chrSize
    # 27
    # use the $chrSize in this sed
    sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
         | hgLoadSqlTab regenRn0 ucscToINSDC stdin ucscToINSDC.bed
     # should be the same for ucscToRefSeq:
    export chrSize=`cut -f1 ucscToRefSeq.bed | awk '{print length($0)}' | sort -n | tail -1`
    echo $chrSize
    # 27
    sed -e "s/21/$chrSize/" $HOME/kent/src/hg/lib/ucscToINSDC.sql \
       | sed -e 's/INSDC/RefSeq/g;' \
         | hgLoadSqlTab regenRn0 ucscToRefSeq stdin ucscToRefSeq.bed

    # should be quiet for all OK
    checkTableCoords regenRn0

    # should cover %100 entirely:
    featureBits -countGaps regenRn0 ucscToINSDC
    # 1065365425 bases of 1065365425 (100.000%) in intersection
    featureBits -countGaps regenRn0 ucscToRefSeq
    # 1065365425 bases of 1065365425 (100.000%) in intersection

#########################################################################
# add chromAlias table (DONE - 2019-06-28 - Hiram)

    mkdir /hive/data/genomes/regenRn0/bed/chromAlias
    cd /hive/data/genomes/regenRn0/bed/chromAlias

    ln -s ../../ucsc/ucsc.regeneron.name.translate regen.tab
    ~/kent/src/hg/utils/automation/chromAlias.pl regen.tab \
	> regenRn0.chromAlias.tab

    join regen.tab <(sort -k1,1 ../../chrom.sizes) \
      | awk '{printf "%s\t0\t%d\t%s\n", $1, $3, $2}' > regen.alias.bed

     wc -l *
#	6846 regen.alias.bed
#	6846 regen.tab
#	6846 regenRn0.chromAlias.tab

    hgLoadSqlTab regenRn0 chromAlias ~/kent/src/hg/lib/chromAlias.sql \
        regenRn0.chromAlias.tab

    # display the Regeneron AGP file as a track:

    ln -s ../../ucsc/ucsc.agp ./translatedRegen.agp

    grep -v "^#" translatedRegen.agp | grep -w scaffold \
      | awk '{printf "%s\t%d\t%d\tgap\t0\t.\n", $1, $2-1, $3}' > regen.gaps.bed

    grep -v "^#" translatedRegen.agp | grep -v -w scaffold \
      | awk '{printf "%s\t%d\t%d\t%s\t0\t%s\n", $1, $2-1, $3, $6, $9}' \
        > regen.contigs.bed

    sort -k1,1 -k2,2n regen.gaps.bed regen.contigs.bed > regen.agp.bed

    hgLoadBed regenRn0 regenAGP regen.agp.bed
    # Read 17962 elements of size 6 from regen.agp.bed

    cut -f1-4 regen.gaps.bed | hgLoadBed regenRn0 regenAGPGap stdin
    # Read 5558 elements of size 4 from stdin

#########################################################################
# fixup search rule for assembly track/gold table (DONE - 2019-06-28 - Hiram)
    cd ~/kent/src/hg/makeDb/trackDb/rat/regenRn0
    # preview prefixes and suffixes:
    hgsql -N -e "select frag from gold;" regenRn0 \
      | sed -e 's/[0-9_FR]\+//;' | sort | uniq -c 
   6725 pi
     67 pisub
  47725 ss

    # implies a rule: '[ps][is](sub)?[0-9]+(_[0-9FR]+)?'

    # verify this rule will find them all and eliminate them all:
    hgsql -N -e "select frag from gold;" regenRn0 | wc -l
    # 54517

    hgsql -N -e "select frag from gold;" regenRn0 \
       | egrep -e '[ps][is](sub)?[0-9]+(_[0-9FR]+)?' | wc -l
    # 54517

    hgsql -N -e "select frag from gold;" regenRn0 \
       | egrep -v -e '[ps][is](sub)?[0-9]+(_[0-9FR]+)?' | wc -l
    # 0

    # hence, add to trackDb/chicken/regenRn0/trackDb.ra
searchTable gold
shortCircuit 1
termRegex [ps][is](sub)?[0-9]+(_[0-9FR]+)?
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 - 2019-06-28 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/repeatMasker
    cd /hive/data/genomes/regenRn0/bed/repeatMasker
    time  (doRepeatMasker.pl -buildDir=`pwd` \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -smallClusterHub=ku regenRn0) > do.log 2>&1 &
    # real    48m25.181s

    cat faSize.rmsk.txt
#2762428432 bases (227617579 N's 2534810853 real 1422483022 upper
#	1112327831 lower) in 6846 sequences in 1 files
#Total size: mean 403509.8 sd 6476189.8 min 101 (pi012238F)
#	max 248247500 (ss100001) median 10668
# %40.27 masked total, %43.88 masked real

    egrep -i "versi|relea" do.log
# RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $
#    February 01 2017 (open-4-0-8) 1.332 version of RepeatMasker
# grep RELEASE /hive/data/staging/data/RepeatMasker/Libraries/RepeatMaskerLib.embl
# CC    Dfam_Consensus RELEASE 20181026;                            *

    time featureBits -countGaps regenRn0 rmsk
    # 1112341443 bases of 2762428432 (40.267%) in intersection
    # real    0m35.822s

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

    # faster way to get the same result on high contig count assemblies:
    time hgsql -N -e 'select genoName,genoStart,genoEnd from rmsk;' regenRn0 \
        | bedSingleCover.pl stdin | ave -col=4 stdin | grep "^total"
    # total 1112341443.000000
    # real    0m20.990s

##########################################################################
# running simple repeat (DONE - 2019-06-28 - Hiram)

    # The '-trf409 4' is a bit smaller than human which is 6

    mkdir /hive/data/genomes/regenRn0/bed/simpleRepeat
    cd /hive/data/genomes/regenRn0/bed/simpleRepeat
    time (doSimpleRepeat.pl -buildDir=`pwd` -bigClusterHub=ku \
        -dbHost=hgwdev -workhorse=hgwdev -smallClusterHub=ku \
        -trf409=4 regenRn0) > do.log 2>&1 &
    # real    58m3.288s

    cat fb.simpleRepeat
    # 91165405 bases of 2534810853 (3.597%) in intersection

    cd /hive/data/genomes/regenRn0
    # when using the Window Masker result:
    cd /hive/data/genomes/regenRn0
#    twoBitMask bed/windowMasker/regenRn0.cleanWMSdust.2bit \
#       -add bed/simpleRepeat/trfMask.bed  regenRn0.2bit
    #   you can safely ignore the warning about fields >= 13

    # or using the rmsk result after it is done:
    twoBitMask regenRn0.rmsk.2bit \
        -add bed/simpleRepeat/trfMask.bed regenRn0.2bit
    #   you can safely ignore the warning about fields >= 13
    twoBitToFa regenRn0.2bit stdout | faSize stdin > faSize.regenRn0.2bit.txt
    cat faSize.regenRn0.2bit.txt
# 2762428432 bases (227617579 N's 2534810853 real 1418746093 upper
#	1116064760 lower) in 6846 sequences in 1 files
# Total size: mean 403509.8 sd 6476189.8 min 101 (pi012238F)
#	max 248247500 (ss100001) median 10668
# %40.40 masked total, %44.03 masked real

    rm /gbdb/regenRn0/regenRn0.2bit
    ln -s `pwd`/regenRn0.2bit /gbdb/regenRn0/regenRn0.2bit

#########################################################################
# CREATE MICROSAT TRACK (DONE - 2019-06-29 - Hiram)
    ssh hgwdev
    mkdir /cluster/data/regenRn0/bed/microsat
    cd /cluster/data/regenRn0/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 regenRn0 microsat microsat.bed
    # Read 228853 elements of size 4 from microsat.bed

##########################################################################
## WINDOWMASKER (DONE - 2019-06-28 - Hiram)
    # wait for RepeatMasker to finish before this, since this is going
    # to compare itself with the rmsk result

    mkdir /hive/data/genomes/regenRn0/bed/windowMasker
    cd /hive/data/genomes/regenRn0/bed/windowMasker
    time (doWindowMasker.pl -buildDir=`pwd` -workhorse=hgwdev \
        -dbHost=hgwdev regenRn0) > do.log 2>&1
    # real    26m58.753s

    # Masking statistics
    cat faSize.regenRn0.cleanWMSdust.txt
# 2762428432 bases (227617579 N's 2534810853 real 1629368138 upper
#	905442715 lower) in 6846 sequences in 1 files
# Total size: mean 403509.8 sd 6476189.8 min 101 (pi012238F)
#	max 248247500 (ss100001) median 10668
# %32.78 masked total, %35.72 masked real

    cat fb.regenRn0.rmsk.windowmaskerSdust.txt
    # 696560115 bases of 2762428432 (25.215%) in intersection

##########################################################################
# cpgIslands - (DONE - 2019-06-29 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/cpgIslands
    cd /hive/data/genomes/regenRn0/bed/cpgIslands
    time (doCpgIslands.pl -dbHost=hgwdev -bigClusterHub=ku \
      -workhorse=hgwdev -smallClusterHub=ku regenRn0) > do.log 2>&1
    # real    3m59.256s

    cat fb.regenRn0.cpgIslandExt.txt
    # 10317331 bases of 2534810853 (0.407%) in intersection

##############################################################################
# genscan - (DONE - 2019-06-29 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/genscan
    cd /hive/data/genomes/regenRn0/bed/genscan
    time (doGenscan.pl -buildDir=`pwd` -workhorse=hgwdev -dbHost=hgwdev \
      -bigClusterHub=ku regenRn0) > do.log 2>&1
    # real    126m0.077s

    cat fb.regenRn0.genscan.txt
    # 54712419 bases of 2534810853 (2.158%) in intersection

    cat fb.regenRn0.genscanSubopt.txt
    # 56830306 bases of 2534810853 (2.242%) in intersection

#########################################################################
# Create kluster run files (DONE - 2019-06-29 - Hiram)

    # numerator is regenRn0 gapless bases "real" as reported by:
    featureBits -noRandom -noHap regenRn0 gap
    # 227617579 bases of 2534810853 (8.980%) 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 \( 2534810853 / 2861349177 \) \* 1024
    #  ( 2534810853 / 2861349177 ) * 1024 = 907.140706

    # ==> use -repMatch=350 according to size scaled down from 1024 for human.
    #   and rounded down to nearest 50
    cd /hive/data/genomes/regenRn0
    blat regenRn0.2bit \
         /dev/null /dev/null -tileSize=11 -makeOoc=jkStuff/regenRn0.11.ooc \
        -repMatch=900
    #   Wrote 29409 overused 11-mers to jkStuff/regenRn0.11.ooc
    # rn6 was repMatch 1000 and:
    #   Wrote 27021 overused 11-mers to jkStuff/rn6.11.ooc
    #   rn5 at repMatch 950: Wrote 34513 overused 11-mers to jkStuff/rn5.11.ooc
    

    #   check non-bridged gaps to see what the typical size is:
    hgsql -N \
        -e 'select * from gap where bridge="no" order by size;' regenRn0 \
        | sort -k7,7nr | ave -col=7 stdin
    # min 51690.000000
    # max 136961.000000

    gapToLift -verbose=2 -minGap=50000 regenRn0 jkStuff/nonBridged.lift \
        -bedFile=jkStuff/nonBridged.bed
    wc -l jkStuff/nonBri*
    # 6866 jkStuff/nonBridged.bed
    # 6866 jkStuff/nonBridged.lift

########################################################################
# lastz/chain/net swap human/hg38 (TBD - 2019-06-28 - Hiram)
    # original alignment
    cd /hive/data/genomes/hg38/bed/lastzRegenRn0.2019-06-28

    cat fb.hg38.chainRegenRn0Link.txt
    # 154079940 bases of 3095998939 (4.977%) in intersection
    cat fb.hg38.chainSynRegenRn0Link.txt
    # 95877644 bases of 3095998939 (3.097%) in intersection
    cat fb.hg38.chainRBest.RegenRn0.txt
    # 106665747 bases of 3095998939 (3.445%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/regenRn0/bed/blastz.hg38.swap
    cd /hive/data/genomes/regenRn0/bed/blastz.hg38.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/hg38/bed/lastzRegenRn0.2019-06-28/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    9m45.514s

    cat fb.regenRn0.chainHg38Link.txt
    # 120955955 bases of 1055588482 (11.459%) in intersection

    cat fb.regenRn0.chainSynHg38Link.txt
    # 92597630 bases of 1055588482 (8.772%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` regenRn0 hg38) > rbest.log 2>&1 &
    # real    139m24.408s

    cat fb.regenRn0.chainRBest.Hg38.txt
    # 106294585 bases of 1055588482 (10.070%) in intersection

#########################################################################
# lastz/chain/net swap mouse/mm10 (TBD - 2019-06-28 - Hiram)

    # original alignment
    cd /hive/data/genomes/mm10/bed/lastzRegenRn0.2019-06-28
    cat fb.mm10.chainRegenRn0Link.txt
    # 101151132 bases of 2652783500 (3.813%) in intersection
    cat fb.mm10.chainSynRegenRn0Link.txt
    # 70707720 bases of 2652783500 (2.665%) in intersection
    cat fb.mm10.chainRBest.RegenRn0.txt 
    # 79649474 bases of 2652783500 (3.002%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/regenRn0/bed/blastz.mm10.swap
    cd /hive/data/genomes/regenRn0/bed/blastz.mm10.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/mm10/bed/lastzRegenRn0.2019-06-28/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    6m41.043s

    cat fb.regenRn0.chainMm10Link.txt
    # 88539346 bases of 1055588482 (8.388%) in intersection

    time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` regenRn0 mm10) > rbest.log 2>&1 &
    # real    94m11.007s

    cat fb.regenRn0.chainRBest.Mm10.txt
    # 79474812 bases of 1055588482 (7.529%) in intersection

#########################################################################
# GENBANK AUTO UPDATE (DONE - 2019-06-29 - Hiram)
    ssh hgwdev
    cd $HOME/kent/src/hg/makeDb/genbank
    git pull
    # /cluster/data/genbank/data/organism.lst shows:
    # #organism       mrnaCnt estCnt  refSeqCnt
    # Rattus norvegicus       130197  1103594 17642

    # edit etc/genbank.conf to add regenRn0 just before galGal5

# regenRn0 (Regeneron rat assembly)
regenRn0.serverGenome = /hive/data/genomes/regenRn0/regenRn0.2bit
regenRn0.ooc = /hive/data/genomes/regenRn0/jkStuff/regenRn0.11.ooc
regenRn0.lift = /hive/data/genomes/regenRn0/jkStuff/nonBridged.lift
regenRn0.refseq.mrna.native.pslCDnaFilter  = ${finished.refseq.mrna.native.pslCDnaFilter}
regenRn0.refseq.mrna.xeno.pslCDnaFilter    = ${finished.refseq.mrna.xeno.pslCDnaFilter}
regenRn0.genbank.mrna.native.pslCDnaFilter = ${finished.genbank.mrna.native.pslCDnaFilter}
regenRn0.genbank.mrna.xeno.pslCDnaFilter   = ${finished.genbank.mrna.xeno.pslCDnaFilter}
regenRn0.genbank.est.native.pslCDnaFilter  = ${finished.genbank.est.native.pslCDnaFilter}
regenRn0.downloadDir = regenRn0
regenRn0.refseq.mrna.xeno.load  = yes
regenRn0.refseq.mrna.xeno.loadDesc = yes
regenRn0.genbank.mrna.xeno.load  = yes
regenRn0.perChromTables = no
regenRn0.mgc = yes
# regenRn0.upstreamGeneTbl = ensGene
# regenRn0.upstreamMaf = multiz13way /hive/data/genomes/regenRn0/bed/multiz13way/species.list.txt

    # verify the files specified exist before checking in the file:
  grep ^regenRn0 etc/genbank.conf | grep hive | awk '{print $NF}' | xargs ls -og
# -rw-rw-r-- 1    247657 Jun 29 17:16 /hive/data/genomes/regenRn0/jkStuff/nonBridged.lift
# -rw-rw-r-- 1    117644 Jun 29 17:13 /hive/data/genomes/regenRn0/jkStuff/regenRn0.11.ooc
# -rw-rw-r-- 1 720490674 Jun 29 16:59 /hive/data/genomes/regenRn0/regenRn0.2bit

    git commit -m "Added regenRn0 - Regeneron rat refs #21579" etc/genbank.conf
    git push
    # update /cluster/data/genbank/:
    make etc-update

    # enable daily alignment and update of hgwdev
    cd ~/kent/src/hg/makeDb/genbank
    git pull
    # add regenRn0 to:
    #   etc/align.dbs etc/hgwdev.dbs
    git add etc/align.dbs etc/hgwdev.dbs
    git commit -m "Added regenRn0 - Regeneron rat refs #21579" etc/hgwdev.dbs
    git push
    make etc-update

    # wait a few days for genbank magic to take place, the tracks will
    # appear

#############################################################################
# augustus gene track (DONE - 2019-06-29 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/augustus
    cd /hive/data/genomes/regenRn0/bed/augustus
    time (doAugustus.pl -buildDir=`pwd` -bigClusterHub=ku \
        -species=human -dbHost=hgwdev \
           -workhorse=hgwdev regenRn0) > do.log 2>&1
    # real    194m56.414s

    cat fb.regenRn0.augustusGene.txt
    # 48867584 bases of 2534810853 (1.928%) in intersection

#########################################################################
# ncbiRefSeq (TBD - 2019-06-28 - Hiram)

    mkdir /hive/data/genomes/regenRn0/bed/ncbiRefSeq
    cd /hive/data/genomes/regenRn0/bed/ncbiRefSeq
    # running step wise just to be careful
    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
      -bigClusterHub=ku -dbHost=hgwdev \
      -stop=download -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
      refseq vertebrate_other Gallus_gallus \
      GCF_000002315.5_GRCg6a regenRn0) > download.log 2>&1
    # real    1m19.029s

    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
      -continue=process -bigClusterHub=ku -dbHost=hgwdev \
      -stop=process -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
      refseq vertebrate_other Gallus_gallus \
      GCF_000002315.5_GRCg6a regenRn0) > process.log 2>&1
    # real    2m6.030s

    time (~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \
      -continue=load -bigClusterHub=ku -dbHost=hgwdev \
      -stop=load -fileServer=hgwdev -smallClusterHub=ku -workhorse=hgwdev \
      refseq vertebrate_other Gallus_gallus \
      GCF_000002315.5_GRCg6a regenRn0) > load.log 2>&1
    # real    0m22.312s

    cat fb.ncbiRefSeq.regenRn0.txt
    #  88641893 bases of 1055588482 (8.397%) in intersection

    # need to add: include ../../refSeqComposite.ra alpha
    # to the chicken/regenRn0/trackDb.ra to turn on the track in the browser

    # there was one gene that claimed to have a protein, but the
    # protein sequence was not included in the protein.faa file
    # discovered from joinerCheck
    # manual fix to blank out this one protein, to see the entry
    hgsql -e 'select * from ncbiRefSeqLink where protAcc="NP_989875.1";' regenRn0
    hgsql -e 'update ncbiRefSeqLink set protAcc="" where protAcc="NP_989875.1";' regenRn0
    # this makes the 'protein' link disappear from the gene details page
    # curious that this gene is marked as a non-coding gene anyway ?
    # gene: FET1 at chr4:63,102,774-63,105,516-

    featureBits -enrichment regenRn0 refGene ncbiRefSeq 
 # refGene 1.374%, ncbiRefSeq 8.397%, both 1.370%, cover 99.73%, enrich 11.88x
    featureBits -enrichment regenRn0 ncbiRefSeq refGene
 # ncbiRefSeq 8.397%, refGene 1.374%, both 1.370%, cover 16.32%, enrich 11.88x

    featureBits -enrichment regenRn0 ncbiRefSeqCurated refGene
 # ncbiRefSeqCurated 1.368%, refGene 1.374%, both 1.364%, cover 99.71%, enrich 72.59x
    featureBits -enrichment regenRn0 refGene ncbiRefSeqCurated
 # refGene 1.374%, ncbiRefSeqCurated 1.368%, both 1.364%, cover 99.32%, enrich 72.59x

#########################################################################
# LIFTOVER TO rn6 (DONE - 2019-06-29 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/regenRn0/bed/blat.rn6.2019-06-29
    cd /hive/data/genomes/regenRn0/bed/blat.rn6.2019-06-29
    doSameSpeciesLiftOver.pl -verbose=2 \
        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -ooc=/hive/data/genomes/regenRn0/jkStuff/regenRn0.11.ooc \
         regenRn0 rn6
    time (doSameSpeciesLiftOver.pl -verbose=2 \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -ooc=/hive/data/genomes/regenRn0/jkStuff/regenRn0.11.ooc \
         regenRn0 rn6) > doLiftOverToRn6.log 2>&1
    # about 3 hours 20 minutes

    # see if the liftOver menus function in the browser from regenRn0 to galGal5

    # would like to see this as a track:
    time chainToPsl regenRn0ToRn6.over.chain.gz ../../chrom.sizes \
   /hive/data/genomes/rn6/chrom.sizes ../../regenRn0.2bit \
   /hive/data/genomes/rn6/regenRn0.2bit regenRn0ToRn6.psl
XXX - running - Mon Jul  1 13:33:33 PDT 2019

#########################################################################
# LIFTOVER TO regenRn1 (DONE - 2019-09-09 - Hiram)
    ssh hgwdev
    mkdir /hive/data/genomes/regenRn0/bed/blat.regenRn1.2019-09-09
    cd /hive/data/genomes/regenRn0/bed/blat.regenRn1.2019-09-09
    doSameSpeciesLiftOver.pl -verbose=2 \
        -debug -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -ooc=/hive/data/genomes/regenRn0/jkStuff/regenRn0.11.ooc \
         regenRn0 regenRn1
    time (doSameSpeciesLiftOver.pl -verbose=2 \
        -bigClusterHub=ku -dbHost=hgwdev -workhorse=hgwdev \
        -ooc=/hive/data/genomes/regenRn0/jkStuff/regenRn0.11.ooc \
         regenRn0 regenRn1) > doLiftOverToRegenRn1.log 2>&1
    # real    248m28.261s

  # see if the liftOver menus function in the browser from regenRn0 to regenRn1

    # would like to see this as a track:
    hgLoadChain regenRn0 chainRegenRn1 regenRn0ToRegenRn1.over.chain.gz
    # Loading 71615 chains into regenRn0.chainRegenRn1

    chainSort regenRn0ToRegenRn1.over.chain.gz stdout \
      | chainPreNet stdin \
        /hive/data/genomes/regenRn0/chrom.sizes \
        /hive/data/genomes/regenRn1/chrom.sizes stdout \
      | chainNet stdin -minSpace=1 /hive/data/genomes/regenRn0/chrom.sizes \
        /hive/data/genomes/regenRn1/chrom.sizes stdout /dev/null \
      | netSyntenic stdin noClass.net

  netClass -verbose=0 -noAr noClass.net regenRn0 regenRn1 regenRn0.regenRn1.net

    netFilter -minGap=10 regenRn0.regenRn1.net \
      | hgLoadNet -verbose=0 regenRn0 netRegenRn1 stdin

 featureBits regenRn0 chainRegenRn1Link > fb.regenRn0.chainRegenRn1Link.txt 2>&1

    cat fb.regenRn0.chainRegenRn1Link.txt
    # 2436426341 bases of 2534810853 (96.119%) in intersection

#########################################################################
#  BLATSERVERS ENTRY (TBD - 2019-06-28 - 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 ("regenRn0", "blat1a", "17892", "1", "0"); \
	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
	VALUES ("regenRn0", "blat1a", "17893", "0", "1");' \
	    hgcentraltest
    #	test it with some sequence

############################################################################
## reset default position to MEPE gene (egg shell protein)
##  (TBD - 2019-06-28 - Hiram)

    # as found from the galGal5 to regenRn0 liftOver
    ssh hgwdev
    hgsql -e 'update dbDb set defaultPos="chr4:45667017-45672928"
	where name="regenRn0";' hgcentraltest

#########################################################################
# crispr whole genome (WORKING - 2019-07-02 - Hiram)
    mkdir /hive/data/genomes/regenRn0/bed/crisprAll
    cd /hive/data/genomes/regenRn0/bed/crisprAll

    # working on this script, adding the indexFa step:
    time (~/kent/src/hg/utils/automation/doCrispr.pl \
   -stop=indexFa -buildDir=`pwd` -smallClusterHub=ku regenRn0 augustusGene) \
	> indexFa.log 2>&1
XXX - running - Tue Jul  2 11:09:39 PDT 2019
    # real    23m26.694s

    # the large shoulder argument will cause the entire genome to be scanned
~/kent/src/hg/utils/automation/doCrispr.pl -verbose=2 -stop=ranges \
    hg19 knownGene -shoulder=250000000 -tableName=crisprAll -fileServer=hgwdev \
    -buildDir=`pwd` -smallClusterHub=hgwdev-101 -bigClusterHub=ku \
      -workhorse=hgwdev


    time (~/kent/src/hg/utils/automation/doCrispr.pl \
       -continue=ranges -stop=guides -buildDir=`pwd` -smallClusterHub=ku \
           regenRn0 ncbiRefSeq) > guides.log 2>&1
    # real    2m50.758s

    # adding the /dev/shm/ setup rsync for the indexed Fa
    # performed manually to work out the procedure
    time (~/kent/src/hg/utils/automation/doCrispr.pl \
        -continue=specScores -stop=specScores -buildDir=`pwd` \
           -smallClusterHub=ku regenRn0 ncbiRefSeq) > specScores.log

    # had about half of ku for about half this time:
# Completed: 884922 of 884922 jobs
# CPU time in finished jobs:  35872791s  597879.85m  9964.66h  415.19d  1.138 y
# IO & Wait Time:               899261s   14987.69m   249.79h   10.41d  0.029 y
# Average job time:                 42s       0.69m     0.01h    0.00d
# Longest finished job:             88s       1.47m     0.02h    0.00d
# Submission to last job:        48045s     800.75m    13.35h    0.56d


    time find tmp/outGuides -type f | xargs cut -f3-6 > ../specScores.tab
    # real    236m17.220s
    wc -l specScores.tab
    # 66451712 specScores.tab

    time (~/kent/src/hg/utils/automation/doCrispr.pl \
	-continue=effScores -stop=load \
	    -buildDir=`pwd` -smallClusterHub=ku regenRn0 ncbiRefSeq) \
	> load.log
    # real    307m41.143s

#########################################################################
# all.joiner update, downloads and in pushQ - (TBD - 2018-10-17 - Hiram)
xyz
    cd $HOME/kent/src/hg/makeDb/schema
    # verify all the business is done for release
    ~/kent/src/hg/utils/automation/verifyBrowser.pl regenRn0

    # fixup all.joiner until this is a clean output
    joinerCheck -database=regenRn0 -tableCoverage all.joiner
    joinerCheck -database=regenRn0 -times all.joiner
    joinerCheck -database=regenRn0 -keys all.joiner

    # when clean, check in:
    git commit -m 'adding rules for regenRn0 refs #22113' all.joiner
    git push
    # run up a 'make alpha' in hg/hgTables to get this all.joiner file
    # into the hgwdev/genome-test system

    cd /hive/data/genomes/regenRn0
    time (makeDownloads.pl regenRn0) > downloads.log 2>&1
    #  real    10m7.605s

    #   now ready for pushQ entry
    mkdir /hive/data/genomes/regenRn0/pushQ
    cd /hive/data/genomes/regenRn0/pushQ
  time (makePushQSql.pl -redmineList regenRn0) > regenRn0.pushQ.sql 2> stderr.out
    # real    9m58.779s

    # remove the extra chainNet files from the listings:
    sed -i -e "/etNig1/d" redmine.regenRn0.file.list
    sed -i -e "/asAcu1/d" redmine.regenRn0.file.list
    sed -i -e "/etNig1/d" redmine.regenRn0.table.list
    sed -i -e "/onAlb1/d" redmine.regenRn0.table.list
    sed -i -e "/asAcu1/d" redmine.regenRn0.table.list
    sed -i -e "/Stickleback/d" redmine.regenRn0.releaseLog.txt
    sed -i -e "/Tetraodon/d" redmine.regenRn0.releaseLog.txt
    sed -i -e "/sparrow/d" redmine.regenRn0.releaseLog.txt
    # remove the tandemDups and gapOverlap from the file list:
    sed -i -e "/tandemDups/d" redmine.regenRn0.table.list
    sed -i -e "/Tandem Dups/d" redmine.regenRn0.releaseLog.txt
    sed -i -e "/gapOverlap/d" redmine.regenRn0.table.list
    sed -i -e "/Gap Overlaps/d" redmine.regenRn0.releaseLog.txt
    #  real    7m21.629s

    #   check for errors in stderr.out, some are OK, e.g.:
    # WARNING: hgwdev does not have /gbdb/regenRn0/wib/gc5Base.wib
    # WARNING: hgwdev does not have /gbdb/regenRn0/wib/quality.wib
    # WARNING: hgwdev does not have /gbdb/regenRn0/bbi/quality.bw
    # WARNING: regenRn0 does not have seq
    # WARNING: regenRn0 does not have extFile

    # add the path names to the listing files in the redmine issue
    # in the three appropriate entry boxes:

#	/hive/data/genomes/regenRn0/pushQ/redmine.regenRn0.file.list
#	/hive/data/genomes/regenRn0/pushQ/redmine.regenRn0.releaseLog.txt
#	/hive/data/genomes/regenRn0/pushQ/redmine.regenRn0.table.list

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