Commit c068561a authored by Holger Brandl's avatar Holger Brandl

updated kotlin support API dependency

parent f7692962
#!/usr/bin/env kscript #!/usr/bin/env kscript
//DEPS de.mpicbg.scicomp:joblist:0.7 de.mpicbg.scicomp:kutils:0.7 //DEPS de.mpicbg.scicomp.joblist:joblist-kotlin:1.1 de.mpicbg.scicomp:kutils:0.7
// add docopts to local m2 index // add docopts to local m2 index
...@@ -7,7 +7,8 @@ ...@@ -7,7 +7,8 @@
// kotlinc-jvm -classpath $(mvncp org.docopt:docopt:0.6.0-SNAPSHOT) // kotlinc-jvm -classpath $(mvncp org.docopt:docopt:0.6.0-SNAPSHOT)
import de.mpicbg.scicomp.kutils.evalBash import de.mpicbg.scicomp.kutils.evalBash
import joblist.JobConfiguration import de.mpicbg.scicomp.kutils.joblist.JobConfig
import de.mpicbg.scicomp.kutils.joblist.createHtmlReport
import joblist.JobList import joblist.JobList
import org.docopt.Docopt import org.docopt.Docopt
import java.io.File import java.io.File
...@@ -131,11 +132,9 @@ for (fastqFile in fastqFiles) { ...@@ -131,11 +132,9 @@ for (fastqFile in fastqFiles) {
samtools index ${fastqBaseName}.bam samtools index ${fastqBaseName}.bam
""".trimIndent() """.trimIndent()
// todo provide proper walltime here
// slurm memory limit https://rc.fas.harvard.edu/resources/documentation/slurm-memory/ // slurm memory limit https://rc.fas.harvard.edu/resources/documentation/slurm-memory/
// sacct -o MaxRSS -j JOBID // sacct -o MaxRSS -j JOBID
jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "10:00", "", 5, 40000, "", better.files.File(File(".").toPath()))) jl.run(JobConfig(cmd, "star__${fastqBaseName}", "10:00", "", 5, 40000))
// jl.run(JobConfiguration(cmd, "star__${fastqBaseName}", "", "medium", 5, 0, "", better.files.File(File(".").toPath())))
} }
...@@ -145,7 +144,7 @@ jl.waitUntilDone(1000) ...@@ -145,7 +144,7 @@ jl.waitUntilDone(1000)
// http://lampwww.epfl.ch/~michelou/scala/using-scala-from-java.html // http://lampwww.epfl.ch/~michelou/scala/using-scala-from-java.html
joblist.`package$`.`MODULE$`.ImplJobListUtils(jl).createHtmlReport() jl.createHtmlReport()
//// estimate expresssion with http://bioinf.wehi.edu.au/featureCounts/ //// estimate expresssion with http://bioinf.wehi.edu.au/featureCounts/
......
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