Commit af05af46 authored by Holger Brandl's avatar Holger Brandl

fixed memory and walltime

parent 59b6e27e
#!/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())))
}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment