############################################################################
#  BLASTZ/CHAIN/NET Zebra finch vs Chicken (DONE - 2013-11-06,25 - Hiram)
#   use a screen to manage this multi-day job
    screen -S strCam0

    mkdir /hive/data/genomes/strCam0/bed/lastzFalPer1.2013-11-06
    cd /hive/data/genomes/strCam0/bed/lastzFalPer1.2013-11-06

    cat << '_EOF_' > DEF
# Struthio camelus/Ostrich vs. Falco peregrinus
BLASTZ_M=50

# TARGET: Struthio camelus/Ostrich StrCam0
SEQ1_DIR=/hive/data/genomes/strCam0/strCam0.2bit
SEQ1_LEN=/hive/data/genomes/strCam0/chrom.sizes
SEQ1_CHUNK=20000000
SEQ1_LIMIT=100
SEQ1_LAP=10000

# QUERY: Falco peregrinus FalPer1
SEQ2_DIR=/hive/data/genomes/falPer1/falPer1.2bit
SEQ2_LEN=/hive/data/genomes/falPer1/chrom.sizes
SEQ2_CHUNK=20000000
SEQ2_LAP=0
SEQ2_LIMIT=50

BASE=/hive/data/genomes/strCam0/bed/lastzFalPer1.2013-11-06
TMPDIR=/dev/shm
'_EOF_'
    # << this line keeps emacs coloring happy
    # screen
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
        `pwd`/DEF \
	-tRepeats=windowmaskerSdust -qRepeats=windowmaskerSdust \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium > do.log 2>&1
    # real    4618m50.082s

    cat fb.strCam0.chainFalPer1Link.txt
    # 975896802 bases of 1187883366 (82.154%) in intersection

    cd /hive/data/genomes/strCam0/bed
    ln -s lastzFalPer1.2013-11-06 lastz.falPer1

    cd /hive/data/genomes/strCam0/bed/lastzFalPer1.2013-11-06
    time doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        strCam0 falPer1 > rbest.log 2>&1 &
    # about 33 minutes

    #   and then swap
    mkdir /hive/data/genomes/falPer1/bed/blastz.strCam0.swap
    cd /hive/data/genomes/falPer1/bed/blastz.strCam0.swap
    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
        /hive/data/genomes/strCam0/bed/lastzFalPer1.2013-11-06/DEF \
        -swap \
        -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
        -chainMinScore=3000 -chainLinearGap=medium > swap.log 2>&1

    # real    51m54.249s
    cat fb.falPer1.chainStrCam0Link.txt
    # 973284248 bases of 1153404357 (84.384%) in intersection

    cd /hive/data/genomes/falPer1/bed
    ln -s blastz.strCam0.swap lastz.strCam0

    time doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` \
        falPer1 strCam0 > rbest.log 2>&1
    #  real    34m45.214s

############################################################################
##############################################################################
# TransMap V3 tracks. see makeDb/doc/transMapTracks.txt (2014-12-21 markd)
##############################################################################

##############################################################################
# swap lastz/chainNet from melGal5 (DONE - 2017-01-20 - Hiram)

    # alignment falPer1 on melGal5:
    cat fb.melGal5.chainFalPer1Link.txt
    #  854639905 bases of 1093044709 (78.189%) in intersection

    # and for the swap:
    mkdir /hive/data/genomes/falPer1/bed/blastz.melGal5.swap
    cd /hive/data/genomes/falPer1/bed/blastz.melGal5.swap

    time (doBlastzChainNet.pl -verbose=2 \
      /hive/data/genomes/melGal5/bed/lastzFalPer1.2017-01-20/DEF \
        -swap -chainMinScore=5000 -chainLinearGap=loose \
          -workhorse=hgwdev -smallClusterHub=ku -bigClusterHub=ku \
            -syntenicNet) > swap.log 2>&1
    #  real    64m19.073s

    cat fb.falPer1.chainMelGal5Link.txt
    # 826670414 bases of 1153404357 (71.672%) in intersection

    time (doRecipBest.pl -workhorse=hgwdev -buildDir=`pwd` falPer1 melGal5) \
       > rbest.log 2>&1
    #  real    247m39.409s

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