Added example of queuing multiple jobs to torque

example/torque_example.sh

@@ -0,0 +1,85 @@
+#!/bin/bash
+base_dir=/path/to/project/
+ref=$base_dir/ref/mm10.fa
+working_dir=$base_dir/working
+inputs="$base_dir/input1.bam $base_dir/input2.bam $base_dir/input3.bam"
+inputarr=($inputs)
+sample_name=example_torque
+job_prefix=gridss_${sample_name}
+
+mkdir -p $working_dir
+cat > $working_dir/gridss.properties << EOF
+# The default chunk size of 10Mb only gives ~300 units of work
+# reducing to 1Mb gives ~3000 which gives a more even distribution
+# of work across jobs
+chunkSize=1000000
+chunkSequenceChangePenalty=100000
+EOF
+
+# Assumes gridss.sh release artifacts are in $base_dir
+gridss_cmd_common="$base_dir/gridss.sh \
+	-r $ref \
+	-o $base_dir/$sample_name.sv.vcf \
+	-a $base_dir/$sample_name.asm.bam \
+	-j $base_dir/gridss-2.6.3-gridss-jar-with-dependencies.jar \
+	-w $working_dir \
+	-c $working_dir/gridss.properties"
+
+# Create a job array for each input file
+threads=8
+cat > $working_dir/${job_prefix}_preprocess.sh << EOF
+#!/bin/bash
+#PBS -N ${job_prefix}_preprocess
+##PBS -o ${job_prefix}_preprocess
+#PBS -t 1-${#inputarr[@]}
+#PBS -l nodes=1:ppn=$threads,mem=16gb,walltime=144:00:0
+#PBS -j oe
+
+module add bwa samtools R sambamba java
+inputarr=($inputs)
+cd $working_dir
+$gridss_cmd_common -t $threads \
+	-s preprocess \
+	\${inputarr[\$((PBS_ARRAYID -1 ))]}
+EOF
+
+# Create a job array containing assembly jobs
+assembly_jobs=32
+cat > $working_dir/${job_prefix}_assembly.sh << EOF
+#!/bin/bash
+#PBS -N ${job_prefix}_assembly
+##PBS -o ${job_prefix}_assembly
+#PBS -t 1-$assembly_jobs
+#PBS -l nodes=1:ppn=$threads,mem=30gb,walltime=144:00:0
+#PBS -j oe
+module add bwa samtools R sambamba java
+inputarr=($inputs)
+cd $working_dir
+$gridss_cmd_common -t $threads \
+	-s assemble \
+	--jobindex \$((PBS_ARRAYID -1 )) \
+	--jobnodes $assembly_jobs \
+	$inputs
+EOF
+
+# And finally, finish perform assembly gather
+# variant calling, and annotation
+threads=16
+cat > $working_dir/${job_prefix}_call.sh << EOF
+#!/bin/bash
+#PBS -N ${job_prefix}_call
+##PBS -o ${job_prefix}_call
+#PBS -l nodes=1:ppn=$threads,mem=30gb,walltime=144:00:0
+#PBS -j oe
+module add bwa samtools R sambamba java
+inputarr=($inputs)
+cd $working_dir
+$gridss_cmd_common -t $threads \
+	$inputs
+EOF
+
+# queue the jobs up with a job dependency on the previous step
+echo "pbs_id=\$(qsub $working_dir/${job_prefix}_preprocess.sh) ; echo \$pbs_id"
+echo "pbs_id=\$(qsub -W depend=afterokarray:\$pbs_id $working_dir/${job_prefix}_assembly.sh) ; echo \$pbs_id)"
+echo "qsub -W depend=afterokarray:\$pbs_id $working_dir/${job_prefix}_call.sh"
+