# The lastz chainNet alignments were done via scripts and cluster jobs.
# A parasol cluster running on hgwdev fed the lastz/chainNet scripts to
# the ku parasol cluster.

# Working in directory:

cd /hive/data/genomes/galGal6/bed/multiz75way/lastzRun

hgwdev parasol 'runJob' script:
##############################################################################

#!/bin/bash

set -beEu -o pipefail

cd /hive/data/genomes/galGal6/bed/multiz75way/lastzRun

if [ $# -lt 1 ]; then
  printf "usage: runOne abcDefN\n" 1>&2
  printf "where abcDefN is one of the databases to run\n" 1>&2
  exit 255
fi

export BED="/hive/data/genomes/galGal6/bed"

export db=$1
export Db="${db^}"

# printf "# %s -> %s\n" "${db}" "${Db}" 1>&2

export wrkDir=`ls -d ${BED}/lastz${Db}* 2> /dev/null`

if [ "x${wrkDir}y" = "xy" ]; then
  export dateStamp=`date "+%Y-%m-%d"`
  wrkDir="${BED}/lastz${Db}.${dateStamp}"
  printf "./prepOne.pl $db\n" 1>&2
  ./prepOne.pl $db 1>&2
  if [ ! -d "${wrkDir}" ]; then
    printf "# ERROR: failed to mkdir '${wrkDir}'\n" 1>&2
    exit 255
  fi
  printf "cd ${wrkDir}\n" 1>&2
  cd ${wrkDir}
  printf "time (./runAlignment.sh) > do.log 2>&1\n" 1>&2
  time (./runAlignment.sh) > do.log 2>&1
else
  printf "# found: %s\n" "${wrkDir}" 1>&2
fi

printf "# %s done: %s\n" "$db" "`date '+%s %F %T'`" > "/hive/data/genomes/galGal6/bed/multiz75way/lastzRun/results/${db}.txt"
exit $?

##############################################################################
template:

#LOOP
runOne $(path1) {check out exists+ results/$(path1).txt}
#ENDLOOP

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

generate jobList from dbId.list:

gensub2 dbId.list single template jobList

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

The runJob script above uses prepOne.pl to generate the directory
structure and run script for the lastz/chainNet.  See also the prepOne.pl
script in this directory.

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