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Commit 63c00a91 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
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Merge pull request #60 from biopet/fix-BIOPET-637 

Make python script absolute paths
parents 492b52f0 db12161e
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
View file @ 63c00a91
......@@ -33,7 +33,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
* @param script name / location of script
*/
def setPythonScript(script: String) {
pythonScript = new File(script)
pythonScript = new File(script).getAbsoluteFile
if (!pythonScript.exists()) {
setPythonScript(script, "")
} else {
......@@ -48,7 +48,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
*/
def setPythonScript(script: String, subpackage: String) {
pythonScriptName = script
pythonScript = new File(".queue/tmp/" + subpackage + pythonScriptName)
pythonScript = new File(".queue/tmp/" + subpackage + pythonScriptName).getAbsoluteFile
if (!pythonScript.getParentFile.exists) pythonScript.getParentFile.mkdirs
val is = getClass.getResourceAsStream(subpackage + pythonScriptName)
if (is != null) {
......
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