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biopet.biopet
Commits
02e65123
Commit
02e65123
authored
Oct 26, 2016
by
Sander Bollen
Browse files
jobtimelimit in core
parent
21452691
Changes
2
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
02e65123
...
...
@@ -58,6 +58,11 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
*/
var
jobDelayTime
:
Option
[
Int
]
=
config
(
"job_delay_time"
)
/**
* wall clock time limit in seconds for a job
*/
var
jobWallClockTimeLimit
:
Option
[
Int
]
=
config
(
"job_wall_time_limit"
)
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun
=
{
case
jt
:
JobTemplate
=>
...
...
@@ -99,6 +104,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
_pipesJobs
.
foreach
(
_
.
beforeGraph
())
_pipesJobs
.
foreach
(
_
.
internalBeforeGraph
())
jobWallClockTimeLimit
.
foreach
(
x
=>
jobNativeArgs
=
jobNativeArgs
.
toList
:::
List
(
s
"-l h_rt=$x"
))
}
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
View file @
02e65123
...
...
@@ -128,9 +128,7 @@ class FreeC(val root: Configurable) extends BiopetCommandLineFunction with Refer
override
def
defaultCoreMemory
=
50
// wallclock time limit in seconds
var
wallClockTimeLimit
:
Int
=
config
(
"wall_time_limit"
,
namespace
=
"freec"
,
default
=
7200
)
jobNativeArgs
=
jobNativeArgs
.
toList
:::
List
(
s
"-l h_rt=$wallClockTimeLimit"
)
jobWallClockTimeLimit
=
config
(
"job_wall_time_limit"
,
namespace
=
"freec"
,
default
=
7200
)
private
var
configFile
:
File
=
_
...
...
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