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Commit 68beea46 authored by Holger Brandl's avatar Holger Brandl
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Merge remote-tracking branch 'remotes/origin/master' into madmax

parents d3488019 398c04b4
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#!/usr/bin/env kscript
//DEPS org.docopt:docopt:0.6.0-SNAPSHOT de.mpicbg.scicomp:joblist_2.11:0.6-SNAPSHOT de.mpicbg.scicomp.bioinfo:kutils:0.1-SNAPSHOT
//DEPS com.offbytwo:docopt:0.6.0.20150202 de.mpicbg.scicomp:joblist:0.6-SNAPSHOT de.mpicbg.scicomp.bioinfo:kutils:0.1-SNAPSHOT
// add docopts to local m2 index
// git clone https://github.com/docopt/docopt.java && cd docopt.java && mvn clean package install -Dmaven.test.skip=true
......@@ -97,7 +98,10 @@ for (fastqFile in fastqFiles) {
samtools index ${fastqBaseName}.bam
""".trimIndent()
jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "", "medium", 5, "", better.files.File(File(".").toPath())))
// todo provide proper walltime here
// slurm memory limit https://rc.fas.harvard.edu/resources/documentation/slurm-memory/
// sacct -o MaxRSS -j JOBID
jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "5:00:00", "", 5, "--mem 40000", better.files.File(File(".").toPath())))
}
......@@ -122,7 +126,7 @@ joblist.`package$`.`MODULE$`.ImplJobListUtils(jl).createHtmlReport()
// cleanup
evalBash("rm - rf *STARgenome *.Log.progress.out _STARtmp *.SJ.out.tab *Log.out")
evalBash("rm -rf *STARgenome *.Log.progress.out _STARtmp *.SJ.out.tab *Log.out")
// Do reporting and perform bam correlation (but don't wait for the results)
......
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