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biopet.biopet
Commits
f072f096
Commit
f072f096
authored
Sep 13, 2016
by
Peter van 't Hof
Browse files
Adding precommands
parent
ca6efa52
Changes
1
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
f072f096
...
...
@@ -18,7 +18,7 @@ import java.io.{ File, FileInputStream, PrintWriter }
import
java.security.MessageDigest
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.utils.commandline.
{
Gather
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.runtime.ProcessSettings
import
org.ggf.drmaa.JobTemplate
...
...
@@ -40,6 +40,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
def
defaultRemoteCommand
=
"bash"
private
val
remoteCommand
:
String
=
config
(
"remote_command"
,
default
=
defaultRemoteCommand
)
val
preCommands
:
List
[
String
]
=
config
(
"pre_commands"
,
default
=
Nil
)
private
def
changeScript
(
file
:
File
)
:
Unit
=
{
val
lines
=
Source
.
fromFile
(
file
).
getLines
().
toList
val
writer
=
new
PrintWriter
(
file
)
...
...
@@ -219,7 +221,8 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
*/
override
final
def
commandLine
:
String
=
{
preCmdInternal
()
val
cmd
=
cmdLine
+
val
cmd
=
preCommands
.
mkString
(
"\n"
,
"\n"
,
"\n"
)
+
cmdLine
+
stdinFile
.
map
(
file
=>
" < "
+
required
(
file
.
getAbsoluteFile
)).
getOrElse
(
""
)
+
stdoutFile
.
map
(
file
=>
" > "
+
required
(
file
.
getAbsoluteFile
)).
getOrElse
(
""
)
addJobReportBinding
(
"command"
,
cmd
)
...
...
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