Commit 7d179c4e authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
Browse files

Merge pull request #84 from biopet/fix-BIOPET-659

Fixing scatter jobs
parents 11260a4c 190b7590
...@@ -54,7 +54,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -54,7 +54,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
} }
writer.println("set -eubf") writer.println("set -eubf")
writer.println("set -o pipefail") writer.println("set -o pipefail")
writer.println(this.commandLine) writer.println(lines.mkString("\n"))
jobDelayTime.foreach(x => writer.println(s"sleep $x")) jobDelayTime.foreach(x => writer.println(s"sleep $x"))
writer.close() writer.close()
} }
...@@ -99,7 +99,13 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction => ...@@ -99,7 +99,13 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
beforeGraph() beforeGraph()
internalBeforeGraph() internalBeforeGraph()
if (jobOutputFile != null) this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile if (jobOutputFile != null) {
this.commandDirectory = this.jobOutputFile.getAbsoluteFile.getParentFile
this match {
case s: ScatterGatherableFunction => s.scatterGatherDirectory = new File(this.commandDirectory, ".scatter")
case _ =>
}
}
super.freezeFieldValues() super.freezeFieldValues()
} }
......
Subproject commit 86ee6287b66562544e701f9ffa7cbbf0af9f3eba Subproject commit 677d757419f515779766b10149b0e92eff71e5b2
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