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|
#!/bin/sh
#
# Script to bundle goby and required data into a
# suitable format for submission to a SGE queue
#
# Absolute path to this script.
SCRIPT=$(readlink -f $0)
# Absolute path this script is in.
SCRIPT_DIR=$(dirname $SCRIPT)
# Absolute path to the SGE align scripts
ALIGN_SCRIPT_DIR=${SCRIPT_DIR}/align
if [ -z "$1" ]; then
echo "Job name is required"
exit 1
fi
. sge-env.sh
# Local goby locations
GOBY_DIR=${GOBY_DIR:-$SCRIPT_DIR/../..}
if [ ! -e ${GOBY_DIR}/goby.jar ]; then
echo "goby.jar not found!"
exit 2
fi
# The job name identifies the location for the scripts
JOB_TAG=$1
JOB_DIR=$(readlink -f .)/${JOB_TAG}
JOB_RESULTS_DIR=${JOB_RESULTS_DIR:-$(readlink -f .)/${JOB_TAG}-results}
if [ -e ${JOB_DIR} ]; then
echo "The job output directory already exists"
exit 3
fi
if [ ! -r ${REFERENCE} ]; then
echo "WARNING: Reference ${REFERENCE} cannot be read"
fi
# Get the number of bytes in the reads file
if [ -z "${READS}" ] || [ ! -r ${READS} ]; then
echo "WARNING: Reads ${READS} file cannot be read"
READS_SIZE=0
else
READS_SIZE=`/usr/bin/stat --format=%s ${READS}`
fi
echo "Bundling job submission files"
# see if the job needs to split into a job array
if [ -z "${CHUNK_SIZE}" ] || [ ${CHUNK_SIZE} -le 0 ] || [ ${CHUNK_SIZE} -ge ${READS_SIZE} ]; then
echo "Alignment will not be split"
else
NUMBER_OF_JOBS=$((${READS_SIZE} / ${CHUNK_SIZE} + 1))
SGE_ARRAY_DIRECTIVE="#$ -t 1-${NUMBER_OF_JOBS}"
echo "Alignment will run as ${NUMBER_OF_JOBS} jobs"
fi
if [ ! -z "${SGE_STATUS_MAILTO}" ]; then
SGE_MAILTO_DIRECTIVE="#$ -M ${SGE_STATUS_MAILTO}"
fi
# Use a basename that is based on name of the reads file
BASENAME=$(basename $READS .compact-reads)
# Create a somewhat unique tag
# ("stage" of job will be added - index, align, concat)
SGE_JOB_NAME=${JOB_TAG}
# Copy goby and submission scripts to the run directory
/bin/mkdir -p ${JOB_DIR}
/bin/cp ${GOBY_DIR}/goby.jar ${GOBY_DIR}/config/log4j.properties \
${ALIGN_SCRIPT_DIR}/align.sh ${ALIGN_SCRIPT_DIR}/index.sh \
${ALIGN_SCRIPT_DIR}/align-concat.sh ${ALIGN_SCRIPT_DIR}/index-align.sh \
${ALIGN_SCRIPT_DIR}/concat.sh ${ALIGN_SCRIPT_DIR}/index-align-concat.sh \
${SCRIPT_DIR}/sge-env.sh ${JOB_DIR}
# Create job specific scripts from the template files
for FILE in goby-index.qsub goby-align.qsub goby-concat.qsub; do
sed -e "s|%REFERENCE%|${REFERENCE}|" \
-e "s|%READS%|${READS}|" \
-e "s|%SGE_QUEUE%|${SGE_QUEUE}|" \
-e "s|%SGE_MEMORY%|${SGE_MEMORY}|" \
-e "s|%SGE_JVM_FLAGS%|${SGE_JVM_FLAGS}|" \
-e "s|%SGE_ARRAY_DIRECTIVE%|${SGE_ARRAY_DIRECTIVE}|" \
-e "s|%SGE_MAILTO_DIRECTIVE%|${SGE_MAILTO_DIRECTIVE}|" \
-e "s|%REFERENCE_INDEX_NAME%|${REFERENCE_INDEX_NAME}|" \
-e "s|%REFERENCE_INDEX_DIRECTORY%|${REFERENCE_INDEX_DIRECTORY}|" \
-e "s|%ALIGNER%|${ALIGNER}|" \
-e "s|%COLORSPACE%|${COLORSPACE}|" \
-e "s|%CHUNK_SIZE%|${CHUNK_SIZE}|" \
-e "s|%BASENAME%|${BASENAME}|" \
-e "s|%BWA_ALIGNER_PATH%|${BWA_ALIGNER_PATH}|" \
-e "s|%LAST_ALIGNER_PATH%|${LAST_ALIGNER_PATH}|" \
-e "s|%LASTAG_ALIGNER_PATH%|${LASTAG_ALIGNER_PATH}|" \
-e "s|%SGE_JOB_NAME%|${SGE_JOB_NAME}|" \
${ALIGN_SCRIPT_DIR}/templates/${FILE} > ${JOB_DIR}/${FILE}
done
echo "Scripts were written to ${JOB_DIR}"
|
