hisat-build.sh

#!/bin/bash

#--HISAT2-BUILD-----------------------------------------
# hisat2-build 
# This command produces a hisat2index genome index from a genome fasta file
# The name of the reference fasta file(s) must be passed in on the command line
#-----------------------------------------------------------------------------
#----SETTINGS---------------
source "${TAILOR_CONFIG}"
#---------------------------

#----JOB SUBMISSION PARAMETERS---------------------------------------------------------------------
PROCESSORS=6
MEMORY="4096"      # PER PROCESSOR!! - 2048=2G, 4096=4G, 8192=8G, 16384=16G, 32768=32G, 65536=64G
DURATION="3:59"  # HH:MM - 72:00=3 days, 96:00=4 days, 192:00=8 days, 384:00=16 days
QUEUE="short"       # short = max 4 hours;   long = max 30 days
#--------------------------------------------------------------------------------------------------

#----PATHS-----------------------------------------------------------------------------------------
INPUT="${HISAT_BUILD_INPUT}"
OUTPUT="${HISAT_BUILD_OUTPUT}"
SCRIPTS=${OUTPUT}/${JOBS_SCRIPTS_DIR}
JOBS=${OUTPUT}/${JOBS_OUT_DIR}
#--------------------------------------------------------------------------------------------------

#----OUTPUT------------------
if [ ! -d ${OUTPUT} ]; then
    mkdir ${OUTPUT}
fi
if [ ! -d ${SCRIPTS} ]; then
    mkdir ${SCRIPTS}
fi
if [ ! -d ${JOBS} ]; then
    mkdir ${JOBS}
fi
#---------------------------

# Save this version of the config file
configFileName=$(basename ${TAILOR_CONFIG})
cp "${TAILOR_CONFIG}" "${OUTPUT}/${configFileName}.$(date +%F_%R)" 

COMMAND=hisat2-build

COMMAND_LINE="${COMMAND} ${HISAT_BUILD_INPUT} ${HISAT_BUILD_OUTPUT}/${HISAT_BUILD_BASENAME}"

scriptString="mktemp -p ${SCRIPTS} ${COMMAND}.assemblies.XXXXXXXXXXX"
echo -e "\n${scriptString}"
tempScript=`${scriptString}`
echo -e "\n${tempScript}"
chmodString="chmod 777 ${tempScript}"
echo -e `${chmodString}`

echo -e "source loadModules.sh\n\n" > ${tempScript}
echo "$COMMAND_LINE" >> ${tempScript}

if [ $SCHEDULER == "sge" ]; then
    SUBMIT_COMMAND="qsub -q $QUEUE -cwd -S /bin/bash -N ${COMMAND} -pe smp ${PROCESSORS} -l h_rt=${DURATION},s_rt=${DURATION},vf=${MEMORY} -m eas -M ${USER_EMAIL} ${tempScript}"
else
    SUBMIT_COMMAND="bsub -q $QUEUE -J ${COMMAND} -n ${PROCESSORS} -R span[hosts=1] -R rusage[mem=${MEMORY}] -W ${DURATION} -u ${LSB_MAILTO} -B -o ${JOBS}/${COMMAND}.%J.out -e ${JOBS}/${COMMAND}.%J.error bash ${tempScript}"
fi

date=`date`
echo -e "\n# $date\n"      >> ${OUTPUT}/${COMMAND}.jobs.log
echo -e "\n# Job Script\n" >> ${OUTPUT}/${COMMAND}.jobs.log
cat ${tempScript}          >> ${OUTPUT}/${COMMAND}.jobs.log
echo -e "\n# Job Submission\n${SUBMIT_COMMAND}\n" >> ${OUTPUT}/${COMMAND}.jobs.log
echo -e "\n#-------------------------------------------------------------------------------------------------------" >> ${OUTPUT}/${COMMAND}.jobs.log

echo `${SUBMIT_COMMAND}`