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Commit 8ca1fd0f authored by Peter van 't Hof's avatar Peter van 't Hof
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Make python script absolute paths

parent 2c9c7c06
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
View file @ 8ca1fd0f
...@@ -33,7 +33,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction { ...@@ -33,7 +33,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
* @param script name / location of script * @param script name / location of script
*/ */
def setPythonScript(script: String) { def setPythonScript(script: String) {
pythonScript = new File(script) pythonScript = new File(script).getAbsoluteFile
if (!pythonScript.exists()) { if (!pythonScript.exists()) {
setPythonScript(script, "") setPythonScript(script, "")
} else { } else {
...@@ -48,7 +48,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction { ...@@ -48,7 +48,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
*/ */
def setPythonScript(script: String, subpackage: String) { def setPythonScript(script: String, subpackage: String) {
pythonScriptName = script pythonScriptName = script
pythonScript = new File(".queue/tmp/" + subpackage + pythonScriptName) pythonScript = new File(".queue/tmp/" + subpackage + pythonScriptName).getAbsoluteFile
if (!pythonScript.getParentFile.exists) pythonScript.getParentFile.mkdirs if (!pythonScript.getParentFile.exists) pythonScript.getParentFile.mkdirs
val is = getClass.getResourceAsStream(subpackage + pythonScriptName) val is = getClass.getResourceAsStream(subpackage + pythonScriptName)
if (is != null) { if (is != null) {
......
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