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biopet.biopet
Commits
a396e973
Commit
a396e973
authored
Dec 26, 2016
by
Peter van 't Hof
Browse files
Fixed submitting
parent
7413fda3
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
a396e973
...
...
@@ -47,6 +47,11 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
private
def
changeScript
(
file
:
File
)
:
Unit
=
{
val
lines
=
Source
.
fromFile
(
file
).
getLines
().
toList
val
writer
=
new
PrintWriter
(
file
)
remoteCommand
match
{
case
"bash"
=>
writer
.
println
(
"#!/bin/bash"
)
case
"sh"
=>
writer
.
println
(
"#!/bin/sh"
)
case
_
=>
writer
.
println
(
s
"#!$remoteCommand"
)
}
writer
.
println
(
"set -eubf"
)
writer
.
println
(
"set -o pipefail"
)
lines
.
foreach
(
writer
.
println
)
...
...
@@ -66,8 +71,9 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
changeScript
(
new
File
(
jt
.
getArgs
.
head
.
toString
))
jt
.
setRemoteCommand
(
remoteCommand
)
case
ps
:
ProcessSettings
=>
changeScript
(
new
File
(
ps
.
getCommand
.
tail
.
head
))
ps
.
setCommand
(
Array
(
remoteCommand
)
++
ps
.
getCommand
.
tail
)
changeScript
(
new
File
(
ps
.
getCommand
.
last
))
if
(
ps
.
getCommand
.
head
!=
"srun"
)
ps
.
setCommand
(
Array
(
remoteCommand
)
++
ps
.
getCommand
.
tail
)
}
/**
...
...
gatk
@
0c34163e
Compare
35db9b91
...
0c34163e
Subproject commit
35db9b9166fba2bc0d889607ecf12f9e15b40cf2
Subproject commit
0c34163e39441895f83ab7690164407dc1a6181a
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