Merge remote-tracking branch 'remotes/origin/master' into madmax

dge_workflow/star_align.kts

 #!/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)