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MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
13 stars 5 forks source link

qualimap task should specify memory requirements #50

Open pansapiens opened 4 years ago

pansapiens commented 4 years ago

In sikExonicRate.bds, the task:

dep(exonicRate, depFile <- [bamFile, gtfFile, strandInfo], canFail := true, cpus := 2, taskName := "getting Int(ra|er)genic rates for"+bamFile) {

should specify the RAM requirements, mem := 7000000000 (eg for SLURM) like:

dep(exonicRate, depFile <- [bamFile, gtfFile, strandInfo], canFail := true, cpus := 2, mem := 7000000000, taskName := "getting Int(ra|er)genic rates for"+bamFile) {

7 GB for the task (1 GB headroom), since the JVM is given 6 Gb via --java-mem-size=6G.