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biopet.biopet
Commits
043874a8
Commit
043874a8
authored
Mar 05, 2015
by
Peter van 't Hof
Browse files
Possible to not convert executable to CanonicalPath
parent
1571f046
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
043874a8
...
...
@@ -73,6 +73,9 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
super
.
freezeFieldValues
()
}
/** can override this value is executable may not be converted to CanonicalPath */
val
executableToCanonicalPath
=
true
/**
* Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
*/
...
...
@@ -87,7 +90,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if
(
process
.
exitValue
==
0
)
{
executable
=
buffer
.
toString
val
file
=
new
File
(
executable
)
executable
=
file
.
getCanonicalPath
if
(
executableToCanonicalPath
)
executable
=
file
.
getCanonicalPath
else
executable
=
file
.
getAbsolutePath
}
else
{
BiopetQScript
.
addError
(
"executable: '"
+
executable
+
"' not found, please check config"
)
}
...
...
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