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biopet.biopet
Commits
90ca66f2
Commit
90ca66f2
authored
Jun 17, 2014
by
Peter van 't Hof
Browse files
version changes
removing source files from jar packaging
parent
683528bf
Changes
15
Hide whitespace changes
Inline
Side-by-side
biopet-framework/dependency-reduced-pom.xml
View file @
90ca66f2
...
...
@@ -3,13 +3,13 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet-Framework
</artifactId>
<name>
Biopet-Framework
</name>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<url>
http://maven.apache.org
</url>
<build>
<plugins>
...
...
biopet-framework/pom.xml
View file @
90ca66f2
...
...
@@ -4,7 +4,7 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet-Framework
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<packaging>
jar
</packaging>
<name>
Biopet-Framework
</name>
...
...
@@ -13,7 +13,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala
deleted
100644 → 0
View file @
683528bf
package
nl.lumc.sasc.biopet.function
import
java.io.FileOutputStream
import
nl.lumc.sasc.biopet.core._
import
org.broadinstitute.sting.queue.function.CommandLineFunction
import
org.broadinstitute.sting.commandline._
import
java.io.File
import
scala.collection.JavaConversions._
trait
Python
extends
CommandLineFunction
{
@Argument
(
doc
=
"Pyhton exe"
,
shortName
=
"script"
)
var
python_exe
:
String
=
"python"
@Input
(
doc
=
"Pyhton script"
,
shortName
=
"script"
,
required
=
false
)
var
python_script
:
File
=
_
private
var
python_script_name
:
String
=
_
def
setPythonScript
(
script
:
String
,
subpackage
:
String
)
{
python_script_name
=
script
//val pack = getClass.getPackage.toString.replaceAll(".", "/")
//logger.info(pack)
// for (r <- getClass.getClassLoader.getResources("/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/*")) {
// logger.info(r)
// logger.info(r.getContent)
// }
python_script
=
new
File
(
".queue/tmp/"
+
subpackage
+
python_script_name
)
if
(!
python_script
.
getParentFile
.
exists
)
python_script
.
getParentFile
.
mkdirs
val
is
=
getClass
.
getResourceAsStream
(
subpackage
+
python_script_name
)
val
os
=
new
FileOutputStream
(
python_script
)
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
}
def
getPythonCommand
()
:
String
=
{
required
(
python_exe
)
+
required
(
python_script
)
}
}
flexiprep/dependency-reduced-pom.xml
View file @
90ca66f2
...
...
@@ -3,13 +3,13 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Flexiprep
</artifactId>
<name>
Flexiprep
</name>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<url>
http://maven.apache.org
</url>
<build>
<resources>
...
...
flexiprep/nbactions.xml
View file @
90ca66f2
...
...
@@ -10,7 +10,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
-l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
@@ -25,7 +25,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
-l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<jpda.listen>
true
</jpda.listen>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
...
...
@@ -41,7 +41,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json
-l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
flexiprep/pom.xml
View file @
90ca66f2
...
...
@@ -4,7 +4,7 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Flexiprep
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<packaging>
jar
</packaging>
<name>
Flexiprep
</name>
...
...
@@ -13,7 +13,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
@@ -45,7 +45,7 @@
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet-Framework
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
</dependency>
<!-- <dependency>
<groupId>org.broadinstitute.sting</groupId>
...
...
@@ -55,12 +55,6 @@
</dependencies>
<build>
<resources>
<resource>
<directory>
src/main/java
</directory>
<includes>
<include>
**/*
</include>
</includes>
</resource>
<resource>
<directory>
scripts
</directory>
<includes>
...
...
gatk/dependency-reduced-pom.xml
View file @
90ca66f2
...
...
@@ -3,13 +3,13 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Gatk
</artifactId>
<name>
Gatk
</name>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<url>
http://maven.apache.org
</url>
<build>
<resources>
...
...
gatk/examples/test.json
View file @
90ca66f2
{
"inputtype"
:
"rna"
,
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/Downloads/FastQC/fastqc"
},
"
bwa
"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
},
"
star
"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
},
"flexiprep"
:
{
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
},
"cutadapt"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
},
...
...
gatk/pom.xml
View file @
90ca66f2
...
...
@@ -4,7 +4,7 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Gatk
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<packaging>
jar
</packaging>
<name>
Gatk
</name>
...
...
@@ -13,7 +13,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
@@ -45,12 +45,12 @@
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet-Framework
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Mapping
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
</dependency>
<dependency>
<groupId>
org.broadinstitute.sting
</groupId>
...
...
@@ -60,12 +60,6 @@
</dependencies>
<build>
<resources>
<resource>
<directory>
src/main/java
</directory>
<includes>
<include>
**/*
</include>
</includes>
</resource>
<resource>
<directory>
scripts
</directory>
<includes>
...
...
gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala
deleted
100644 → 0
View file @
683528bf
package
nl.lumc.sasc.biopet.pipelines.gatk.modules
import
nl.lumc.sasc.biopet.core._
import
org.broadinstitute.sting.queue.QScript
import
org.broadinstitute.sting.queue.extensions.gatk._
class
BiopetVariantAnnotator
(
private
var
globalConfig
:
Config
)
extends
QScript
with
BiopetQScript
{
qscript
=>
def
this
()
=
this
(
new
Config
())
@Argument
(
doc
=
"Config Json file"
,
shortName
=
"config"
,
required
=
false
)
var
configfiles
:
List
[
File
]
=
Nil
@Argument
(
doc
=
"Reference"
,
shortName
=
"R"
)
var
referenceFile
:
File
=
_
@Argument
(
doc
=
"Variant"
,
shortName
=
"V"
)
var
variants
:
List
[
File
]
=
Nil
@Argument
(
doc
=
"Output directory"
,
shortName
=
"outputDir"
,
required
=
false
)
var
outputDir
:
String
=
_
@Argument
(
doc
=
"Scattercount"
,
shortName
=
"SC"
)
var
scattercount
:
Int
=
0
def
init
{
for
(
file
<-
configfiles
)
globalConfig
.
loadConfigFile
(
file
)
config
=
Config
.
mergeConfigs
(
globalConfig
.
getAsConfig
(
"variantannotator"
),
globalConfig
)
if
(
outputDir
==
null
)
outputDir
=
this
.
qSettings
.
runDirectory
if
(
scattercount
==
0
&&
config
.
contains
(
"scattercount"
))
scattercount
=
config
.
getAsInt
(
"scattercount"
)
}
def
script
{
init
for
(
inputFile
<-
qscript
.
variants
)
{
val
variantAnnotator
=
new
VariantAnnotator
with
gatkArguments
{
val
config
:
Config
=
Config
.
mergeConfigs
(
qscript
.
config
.
getAsConfig
(
"variantannotator"
),
qscript
.
config
)
this
.
variant
=
inputFile
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
.
getAsString
(
"dbsnp"
)
this
.
out
=
swapExt
(
outputDir
,
inputFile
,
".vcf"
,
".annotated.vcf"
)
if
(
qscript
.
scattercount
>
1
)
this
.
scatterCount
=
qscript
.
scattercount
if
(
config
.
contains
(
"scattercount"
))
this
.
scatterCount
=
config
.
getAsInt
(
"scattercount"
)
}
add
(
variantAnnotator
)
}
}
trait
gatkArguments
extends
CommandLineGATK
{
this
.
reference_sequence
=
referenceFile
this
.
memoryLimit
=
2
this
.
jobResourceRequests
:+=
"h_vmem=4G"
}
}
mapping/dependency-reduced-pom.xml
View file @
90ca66f2
...
...
@@ -3,13 +3,13 @@
<parent>
<artifactId>
Biopet
</artifactId>
<groupId>
nl.lumc.sasc
</groupId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
</parent>
<modelVersion>
4.0.0
</modelVersion>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Mapping
</artifactId>
<name>
Mapping
</name>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<url>
http://maven.apache.org
</url>
<build>
<resources>
...
...
mapping/examples/test.json
View file @
90ca66f2
{
"referenceFile"
:
"/blabla/blabla.fa"
,
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/Downloads/FastQC/fastqc"
},
"bwa"
:
{
"exe"
:
"test"
},
"flexiprep"
:
{
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
},
"cutadapt"
:
{
"exe"
:
"/home/pjvan_thof/pipelines/test/test"
},
...
...
mapping/nbactions.xml
View file @
90ca66f2
...
...
@@ -10,7 +10,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
star-2pass
-skipflexiprep
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
bwa
-skipflexiprep
-l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
@@ -25,7 +25,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
star-2pass
-skipflexiprep
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
bwa
-skipflexiprep
-l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<jpda.listen>
true
</jpda.listen>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
...
...
@@ -41,7 +41,7 @@
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
star-2pass
-skipflexiprep
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
bwa
-skipflexiprep
-l DEBUG
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
mapping/pom.xml
View file @
90ca66f2
...
...
@@ -4,7 +4,7 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Mapping
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<packaging>
jar
</packaging>
<name>
Mapping
</name>
...
...
@@ -13,7 +13,7 @@
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<relativePath>
../
</relativePath>
</parent>
...
...
@@ -45,12 +45,12 @@
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet-Framework
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Flexiprep
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
</dependency>
<dependency>
<groupId>
org.broadinstitute.sting
</groupId>
...
...
@@ -60,12 +60,6 @@
</dependencies>
<build>
<resources>
<resource>
<directory>
src/main/java
</directory>
<includes>
<include>
**/*
</include>
</includes>
</resource>
<resource>
<directory>
scripts
</directory>
<includes>
...
...
pom.xml
View file @
90ca66f2
...
...
@@ -3,7 +3,7 @@
<modelVersion>
4.0.0
</modelVersion>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.1.
0
</version>
<version>
0.1.
1
</version>
<packaging>
pom
</packaging>
<name>
Biopet
</name>
<modules>
...
...
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