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biopet.biopet
Commits
63c00a91
Commit
63c00a91
authored
Apr 07, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 07, 2017
Browse files
Merge pull request #60 from biopet/fix-BIOPET-637
Make python script absolute paths
parents
492b52f0
db12161e
Changes
1
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Inline
Side-by-side
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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