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biopet.biopet
Commits
ca601520
Commit
ca601520
authored
Apr 29, 2015
by
Peter van 't Hof
Browse files
Added some scala docs
parent
b04b3390
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala
View file @
ca601520
...
...
@@ -33,7 +33,11 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
checkScript
()
}
def
checkScript
(
local
:
Boolean
=
false
)
:
Unit
=
{
/**
* If script not exist in file system it try to copy it from the jar
* @param local if true it use File.createTempFile instead of ".queue/tmp/"
*/
protected
def
checkScript
(
local
:
Boolean
=
false
)
:
Unit
=
{
if
(
script
.
exists
())
{
script
=
script
.
getAbsoluteFile
}
else
{
...
...
@@ -53,12 +57,24 @@ trait RscriptCommandLineFunction extends BiopetCommandLineFunction {
}
}
/**
* Execute rscript on local system
* @param logger How to handle stdout and stderr
*/
def
runLocal
(
logger
:
ProcessLogger
)
:
Unit
=
{
checkScript
(
local
=
true
)
Process
(
cmdLine
).
run
(
logger
)
}
/**
* Execute rscript on local system
* Stdout and stderr will go to biopet logger
*/
def
runLocal
()
:
Unit
=
{
runLocal
(
ProcessLogger
(
logger
.
info
(
_
)))
}
def
cmdLine
:
String
=
{
required
(
executable
)
+
required
(
script
)
...
...
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