Commit 41f9df22 authored by bow's avatar bow
Browse files

Various fixes for cluster compatibility

parent 6c394efd
......@@ -33,7 +33,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 8
/** default vmem for cluster jobs */
override val defaultVmem = "4G"
override val defaultVmem = "5G"
/** input file */
@Input(doc = "Input file (SAM or BAM)", required = true)
......
......@@ -26,7 +26,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
override val defaultThreads = 8
/** default vmem for cluster jobs */
override val defaultVmem = "4G"
override val defaultVmem = "6G"
/** input file */
@Input(doc = "Input FASTQ file(s)", required = true) //var input: List[File] = _
......@@ -326,10 +326,6 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
override val versionRegex = """.* version (.*)""".r
override def versionCommand = executable + " --version"
override def beforeGraph: Unit = {
threads = nthreads.getOrElse(1)
}
def cmdLine = {
required(executable) +
optional("--dir", dir) +
......
......@@ -80,7 +80,6 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
outputSAindex = new File(prefix + "SAindex")
sjdbOverhang = config("sjdboverhang", 75)
}
threads = runThreadN.getOrElse(1)
}
/** Returns command to execute */
......
......@@ -32,7 +32,7 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
override val versionExitcode = List(0, 1)
override def versionCommand = executable + " --version"
override val defaultVmem = "4G"
override val defaultVmem = "6G"
override val defaultThreads = 8
@Input(doc = "FastQ file(s) R1", shortName = "R1")
......
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