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biopet.biopet
Commits
a332996e
Commit
a332996e
authored
Mar 03, 2015
by
Peter van 't Hof
Browse files
Java jobs now show diffrent version output in summary
parent
ddc6e115
Changes
2
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
View file @
a332996e
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core.summary
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunctionTrait
,
BiopetCommandLineFunction
,
SampleLibraryTag
,
BiopetQScript
}
import
nl.lumc.sasc.biopet.core.
_
import
nl.lumc.sasc.biopet.extensions.Md5sum
import
scala.collection.mutable
...
...
@@ -104,8 +104,13 @@ trait SummaryQScript extends BiopetQScript {
}
//Automatic checksums
for
((
_
,
summarizableList
)
<-
summarizables
;
summarizable
<-
summarizableList
;
(
_
,
file
)
<-
summarizable
.
summaryFiles
)
for
((
_
,
summarizableList
)
<-
summarizables
;
summarizable
<-
summarizableList
;
(
_
,
file
)
<-
summarizable
.
summaryFiles
)
{
addChecksum
(
file
)
summarizable
match
{
case
f
:
BiopetJavaCommandLineFunction
=>
if
(
f
.
jarFile
!=
null
)
addChecksum
(
f
.
jarFile
)
case
_
=>
}
}
for
((
_
,
file
)
<-
this
.
summaryFiles
)
addChecksum
(
file
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
View file @
a332996e
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core.summary
import
java.io.
{
FileInputStream
,
PrintWriter
,
File
}
import
java.security.MessageDigest
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunctionTrait
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
BiopetCommandLineFunction
,
BiopetCommandLineFunctionTrait
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.queue.function.
{
QFunction
,
InProcessFunction
}
...
...
@@ -56,7 +56,12 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
val
executables
:
Map
[
String
,
Any
]
=
{
(
for
(
f
<-
qscript
.
functions
if
f
.
isInstanceOf
[
BiopetCommandLineFunctionTrait
])
yield
{
f
match
{
case
f
:
BiopetCommandLineFunctionTrait
=>
{
case
f
:
BiopetJavaCommandLineFunction
=>
{
f
.
configName
->
Map
(
"version"
->
f
.
getVersion
,
"java_md5"
->
BiopetCommandLineFunctionTrait
.
executableMd5Cache
.
getOrElse
(
f
.
executable
,
None
),
"jar_md5"
->
SummaryQScript
.
md5sumCache
.
getOrElse
(
f
.
jarFile
,
None
))
}
case
f
:
BiopetCommandLineFunction
=>
{
f
.
configName
->
Map
(
"version"
->
f
.
getVersion
,
"md5"
->
BiopetCommandLineFunctionTrait
.
executableMd5Cache
.
getOrElse
(
f
.
executable
,
None
))
}
...
...
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