From e42e39c69d49f7a083545f55644e0559bf757645 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 16 Feb 2015 19:36:21 +0100
Subject: [PATCH] Fix outputDirs
---
.../lumc/sasc/biopet/extensions/Raxml.scala | 23 ++++++++++---------
.../sasc/biopet/extensions/RunGubbins.scala | 5 ++--
2 files changed, 15 insertions(+), 13 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
index 991325495..12a36ad80 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala
@@ -48,7 +48,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
var f: String = "d"
@Argument(doc = "Output directory", required = true)
- var w: String = _
+ var w: File = null
var noBfgs: Boolean = config("no_bfgs", default = false)
@@ -65,6 +65,7 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
var executableThreads: Option[String] = config("exe_pthreads")
override def beforeGraph {
+ require(w != null)
if (threads == 0) threads = getThreads(defaultThreads)
executable = if (threads > 1 && executableThreads.isDefined) executableThreads.get else executableNonThreads
super.beforeGraph
@@ -73,24 +74,24 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
case "d" if b.isEmpty => {
out +:= getBestTreeFile
for (t <- 0 until N.getOrElse(1)) {
- out +:= new File(w + File.separator + "RAxML_log." + n + ".RUN." + t)
- out +:= new File(w + File.separator + "RAxML_parsimonyTree." + n + ".RUN." + t)
- out +:= new File(w + File.separator + "RAxML_result." + n + ".RUN." + t)
+ out +:= new File(w, "RAxML_log." + n + ".RUN." + t)
+ out +:= new File(w, "RAxML_parsimonyTree." + n + ".RUN." + t)
+ out +:= new File(w, "RAxML_result." + n + ".RUN." + t)
}
}
case "d" if b.isDefined => out +:= getBootstrapFile
case "b" => {
- out +:= new File(w + File.separator + "RAxML_bipartitionsBranchLabels." + n)
- out +:= new File(w + File.separator + "RAxML_bipartitions." + n)
+ out +:= new File(w, "RAxML_bipartitionsBranchLabels." + n)
+ out +:= new File(w, "RAxML_bipartitions." + n)
}
case _ =>
}
}
- def getBestTreeFile: File = new File(w + File.separator + "RAxML_bestTree." + n)
- def getBootstrapFile: File = new File(w + File.separator + "RAxML_bootstrap." + n)
- def getBipartitionsFile: File = new File(w + File.separator + "RAxML_bipartitions." + n)
- def getInfoFile: File = new File(w + File.separator + "RAxML_info." + n)
+ def getBestTreeFile: File = new File(w, "RAxML_bestTree." + n)
+ def getBootstrapFile: File = new File(w, "RAxML_bootstrap." + n)
+ def getBipartitionsFile: File = new File(w, "RAxML_bipartitions." + n)
+ def getInfoFile: File = new File(w, "RAxML_info." + n)
def cmdLine = required(executable) +
required("-m", m) +
@@ -103,6 +104,6 @@ class Raxml(val root: Configurable) extends BiopetCommandLineFunction {
optional("-f", f) +
optional("-t", t) +
optional("-z", z) +
- conditional(noBfgs, "--no-bgfs") +
+ conditional(noBfgs, "--no-bfgs") +
required("-T", threads)
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
index a041f5dc7..454572dab 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala
@@ -33,7 +33,7 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
var outputFiles: List[File] = Nil
@Argument(required = true)
- var outputDirectory: String = _
+ var outputDirectory: File = null
executable = config("exe", default = "run_gubbins.py")
var outgroup: Option[String] = config("outgroup")
@@ -49,7 +49,8 @@ class RunGubbins(val root: Configurable) extends BiopetCommandLineFunction {
override def beforeGraph: Unit = {
super.beforeGraph
- jobLocalDir = new File(outputDirectory)
+ require(outputDirectory != null)
+ jobLocalDir = outputDirectory
if (prefix.isEmpty) prefix = Some(fastafile.getName)
val out: List[String] = List(".recombination_predictions.embl",
".recombination_predictions.gff",
--
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