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biopet.biopet
Commits
c30670ae
Commit
c30670ae
authored
Mar 23, 2015
by
bow
Browse files
Use package version in Gentrap
parent
d190b9e2
Changes
1
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public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
View file @
c30670ae
...
...
@@ -16,7 +16,6 @@
package
nl.lumc.sasc.biopet.pipelines.gentrap
import
java.io.File
import
java.util.Properties
import
scala.language.reflectiveCalls
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -24,6 +23,7 @@ import org.broadinstitute.gatk.queue.function.QFunction
import
picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
import
scalaz._
,
Scalaz
.
_
import
nl.lumc.sasc.biopet.FullVersion
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.core.summary._
...
...
@@ -234,16 +234,6 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
"isoform_fpkm_cufflinks_blind_heatmap"
->
isoFpkmCufflinksBlindHeatmapJob
)
private
def
version
:
String
=
{
val
baseVersion
=
getClass
.
getPackage
.
getImplementationVersion
val
commitHash
=
{
val
prop
=
new
Properties
()
prop
.
load
(
getClass
.
getClassLoader
.
getResourceAsStream
(
"git.properties"
))
prop
.
getProperty
(
"git.commit.id.abbrev"
)
}
s
"$baseVersion ($commitHash)"
}
/** Output summary file */
def
summaryFile
:
File
=
new
File
(
outputDir
,
"gentrap.summary.json"
)
...
...
@@ -268,7 +258,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
"strand_protocol"
->
strandProtocol
.
toString
,
"call_variants"
->
callVariants
,
"remove_ribosomal_reads"
->
removeRibosomalReads
,
"version"
->
v
ersion
"version"
->
FullV
ersion
)
/** Job for writing PDF report template */
...
...
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