Commit ea348cd6 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed version command

parent 086d5af1
......@@ -32,7 +32,11 @@ class KrakenReport(val root: Configurable) extends BiopetCommandLineFunction wit
override def defaultCoreMemory = 4.0
override def defaultThreads = 1
def versionCommand = new File(new File(executable).getParent, "kraken").getAbsolutePath + " --version"
def versionCommand = {
val exe = new File(new File(executable).getParent, "kraken")
if (exe.exists()) exe.getAbsolutePath + " --version"
else executable + " --version"
}
var db: File = config("db")
var show_zeros: Boolean = config("show_zeros", default = false)
......@@ -43,10 +47,9 @@ class KrakenReport(val root: Configurable) extends BiopetCommandLineFunction wit
@Output(doc = "Output path kraken report")
var output: File = _
def cmdLine: String = {
val cmd: String = required(executable) + "--db " + required(db) +
conditional(show_zeros, "--show-zeros") +
required(input.getAbsolutePath) + " > " + required(output.getAbsolutePath)
cmd
}
def cmdLine: String = required(executable) +
required("--db", db) +
conditional(show_zeros, "--show-zeros") +
required(input) +
" > " + required(output)
}
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