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biopet.biopet
Commits
db4dcbca
Commit
db4dcbca
authored
Oct 26, 2015
by
Peter van 't Hof
Browse files
Style changes
parent
66f1b6ec
Changes
1
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
db4dcbca
...
...
@@ -26,7 +26,6 @@ import org.ggf.drmaa.JobTemplate
import
scala.collection.mutable
import
scala.io.Source
import
scala.sys.process.
{
Process
,
ProcessLogger
}
import
scala.util.matching.Regex
import
scala.collection.JavaConversions._
/** Biopet command line trait to auto check executable and cluster values */
...
...
@@ -50,20 +49,18 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
val
writer
=
new
PrintWriter
(
file
)
writer
.
println
(
"set -eubf"
)
writer
.
println
(
"set -o pipefail"
)
lines
.
foreach
(
writer
.
println
(
_
)
)
lines
.
foreach
(
writer
.
println
)
writer
.
close
()
}
// This overrides the default "sh" from queue. For Biopet the default is "bash"
updateJobRun
=
{
case
jt
:
JobTemplate
=>
{
case
jt
:
JobTemplate
=>
changeScript
(
new
File
(
jt
.
getArgs
.
head
.
toString
))
jt
.
setRemoteCommand
(
remoteCommand
)
}
case
ps
:
ProcessSettings
=>
{
case
ps
:
ProcessSettings
=>
changeScript
(
new
File
(
ps
.
getCommand
.
tail
.
head
))
ps
.
setCommand
(
Array
(
remoteCommand
)
++
ps
.
getCommand
.
tail
)
}
}
/**
...
...
@@ -135,10 +132,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
that
.
beforeGraph
()
that
.
internalBeforeGraph
()
this
match
{
case
p
:
BiopetPipe
=>
{
case
p
:
BiopetPipe
=>
p
.
commands
.
last
.
_outputAsStdout
=
true
new
BiopetPipe
(
p
.
commands
:::
that
::
Nil
)
}
case
_
=>
new
BiopetPipe
(
List
(
this
,
that
))
}
}
...
...
@@ -209,7 +205,6 @@ object BiopetCommandLineFunction extends Logging {
if
(
executable
!=
null
)
{
if
(!
BiopetCommandLineFunction
.
executableCache
.
contains
(
executable
))
{
try
{
val
oldExecutable
=
executable
val
buffer
=
new
StringBuffer
()
val
cmd
=
Seq
(
"which"
,
executable
)
val
process
=
Process
(
cmd
).
run
(
ProcessLogger
(
buffer
.
append
(
_
)))
...
...
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