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|
#!/bin/sh
# Submit to the rascals queue
#$ -q *@@rascals.h
# Name of the job
#$ -N %SGE_JOB_NAME%-align
# Execute the script from the current directory
#$ -cwd
# Combine SGE error and output files.
#$ -j y
# Memory resource requirements
#$ -l h_vmem=%SGE_MEMORY%
# Mail job begin status
#$ -m b
# Mail job completion status
#$ -m e
%SGE_MAILTO_DIRECTIVE%
%SGE_ARRAY_DIRECTIVE%
#
# Output some useful SGE job information
#
echo ------------------------------------------------------
echo SGE: qsub is running on ${SGE_O_HOST}
echo SGE: originating queue is ${QUEUE}
echo SGE: executing cell is ${SGE_CELL}
echo SGE: working directory is ${SGE_O_WORKDIR}
echo SGE: execution mode is ${ENVIRONMENT}
echo SGE: execution host is ${HOSTNAME}
echo SGE: job identifier is ${JOB_ID}
echo SGE: job name is ${JOB_NAME}
echo SGE: task number is ${SGE_TASK_ID}
echo SGE: current home directory is ${SGE_O_HOME}
echo SGE: scratch directory is ${TMPDIR}
echo SGE: PATH = ${SGE_O_PATH}
echo ------------------------------------------------------
# Pull in softlib commands
. /etc/profile
# The reference file to align with
REFERENCE=%REFERENCE%
REFERENCE_FILE=${REFERENCE##*/}
REFERENCE_INDEX_NAME=${REFERENCE_FILE%.*}.fasta
REFERENCE_INDEX_DIRECTORY=%REFERENCE_INDEX_DIRECTORY%
# The reads file to process
READS=%READS%
READS_FILE=${READS##*/}
# Copy the goby and support tools to the local node
# TODO: copy bwa etc.
/bin/cp ${SGE_O_WORKDIR}/goby.jar ${SGE_O_WORKDIR}/log4j.properties ${TMPDIR}
# Extract the reads if a split is needed
if [ ! -z ${SGE_TASK_ID} ] && [ "${SGE_TASK_ID}" != "undefined" ]; then
CHUNK_SIZE=%CHUNK_SIZE%
START_POSITION=$(($((SGE_TASK_ID - 1)) * $CHUNK_SIZE))
END_POSITION=$(($START_POSITION + $CHUNK_SIZE - 1))
cd ${TMPDIR}
java %SGE_JVM_FLAGS% -Dlog4j.debug=true -Dlog4j.configuration=file:log4j.properties \
-Dexecutables.path.bwa=%BWA_ALIGNER_PATH% -Dexecutables.path.last=%LAST_ALIGNER_PATH% \
-Dexecutables.path.lastag=%LASTAG_ALIGNER_PATH% \
-jar goby.jar --mode reformat-compact-reads --output ${READS_FILE} \
--start-position ${START_POSITION} --end-position ${END_POSITION} ${READS}
else
/bin/cp ${READS} ${TMPDIR}
fi
# Run the alignment
cd ${TMPDIR}
java %SGE_JVM_FLAGS% -Dlog4j.debug=true -Dlog4j.configuration=file:log4j.properties \
-Dexecutables.path.bwa=%BWA_ALIGNER_PATH% -Dexecutables.path.last=%LAST_ALIGNER_PATH% \
-Dexecutables.path.lastag=%LASTAG_ALIGNER_PATH% \
-jar goby.jar --mode align %COLORSPACE% --reference ${REFERENCE} --aligner %ALIGNER% --search \
--database-name ${REFERENCE_INDEX_NAME} --database-directory ${REFERENCE_INDEX_DIRECTORY} \
--reads ${READS_FILE} --basename %BASENAME%
# Copy the results back
if [ -z ${SGE_TASK_ID} ] || [ "${SGE_TASK_ID}" == "undefined" ]; then
RESULT_DIR=${SGE_O_WORKDIR}/results/%BASENAME%
else
RESULT_DIR=${SGE_O_WORKDIR}/split-results/%BASENAME%-${SGE_TASK_ID}
fi
/bin/mkdir -p ${RESULT_DIR}
/bin/cp *.entries *.header *.stats *.tmh ${RESULT_DIR}
|
