https://github.com/arjunrajlaboratory/RajLabSeqTools
Tip revision: f267e82b2edd18a28926b84fc23cb2b55bdbc9c3 authored by Ian Mellis on 05 January 2016, 20:38:56 UTC
Updated runHTSeq.sh to call shared version of hg19.gtf, rather than Syd's in CancerSeq repo. Made a note on Rajlabseqtools pipeline doc.
Updated runHTSeq.sh to call shared version of hg19.gtf, rather than Syd's in CancerSeq repo. Made a note on Rajlabseqtools pipeline doc.
Tip revision: f267e82
submitGenerateCounts.sh
#!
# run from within repo
cmdToRun="$codeHomeDir/rajlabseqtools/Utilities/stepThreeGenerateCounts/allGenerateCounts.sh $EXPERIMENT $codeHomeDir $PROJECT $gtfFile"
JOB_ARRAY_PARAMETER_TEMPLATE="generateCounts[1-tk]"
#The expression within ${} below replaces "tk" with the correct number of samples (defined in the setEnvironmentVariables.sh script)
bsub -J ${JOB_ARRAY_PARAMETER_TEMPLATE/tk/$N_SAMPLES} -o out.%I -e err.%I $cmdToRun
