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biopet.biopet
Commits
4f6ea975
Commit
4f6ea975
authored
Aug 25, 2014
by
Peter van 't Hof
Browse files
Added BiopetPackage as complete package
parent
33b1e8fc
Changes
9
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.gitignore
View file @
4f6ea975
dependency-reduced-pom.xml
*~
*.swp
/Biopet/nbproject/private/
/Biopet/build/
\ No newline at end of file
biopet-package/.gitignore
0 → 100644
View file @
4f6ea975
/target/
\ No newline at end of file
biopet-package/nbactions.xml
0 → 100644
View file @
4f6ea975
<?xml version="1.0" encoding="UTF-8"?>
<actions>
<action>
<actionName>
run
</actionName>
<packagings>
<packaging>
jar
</packaging>
</packagings>
<goals>
<goal>
process-classes
</goal>
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.core.BiopetExecuteble flexiprep
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
</action>
<action>
<actionName>
debug
</actionName>
<packagings>
<packaging>
jar
</packaging>
</packagings>
<goals>
<goal>
process-classes
</goal>
<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.core.BiopetExecuteble flexiprep
</exec.args>
<exec.executable>
java
</exec.executable>
<jpda.listen>
true
</jpda.listen>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
</action>
<action>
<actionName>
profile
</actionName>
<packagings>
<packaging>
jar
</packaging>
</packagings>
<goals>
<goal>
process-classes
</goal>
<goal>
org.codehaus.mojo:exec-maven-plugin:1.2.1:exec
</goal>
</goals>
<properties>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.core.BiopetExecuteble flexiprep
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
</action>
</actions>
biopet-package/pom.xml
0 → 100644
View file @
4f6ea975
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
<modelVersion>
4.0.0
</modelVersion>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetPackage
</artifactId>
<version>
0.1.3
</version>
<packaging>
jar
</packaging>
<name>
BiopetPackage
</name>
<url>
http://maven.apache.org
</url>
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet
</artifactId>
<version>
0.1.3
</version>
<relativePath>
../
</relativePath>
</parent>
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
<sting.unpack.phase>
prepare-package
</sting.unpack.phase>
<sting.shade.phase>
package
</sting.shade.phase>
<app.main.class>
nl.lumc.sasc.biopet.pipelines.pipelinetemplate.BiopetPackage
</app.main.class>
</properties>
<dependencies>
<dependency>
<groupId>
org.scala-lang
</groupId>
<artifactId>
scala-compiler
</artifactId>
<version>
2.11.0
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Biopet-Framework
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Flexiprep
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Gentrap
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Mapping
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Bam-Metrics
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
GatkGenotyping
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
GatkVariantcalling
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
GatkVcfSampleCompare
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
GatkBenchmarkGenotyping
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
GatkPipeline
</artifactId>
<version>
0.1.3
</version>
</dependency>
<dependency>
<groupId>
org.broadinstitute.gatk
</groupId>
<artifactId>
gatk-queue-package-distribution
</artifactId>
<version>
3.2
</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>
src/main/scripts
</directory>
<includes>
<include>
**/*
</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>
org.scala-tools
</groupId>
<artifactId>
maven-scala-plugin
</artifactId>
<version>
2.15.2
</version>
<executions>
<execution>
<id>
scala-compile
</id>
<goals>
<goal>
compile
</goal>
<goal>
testCompile
</goal>
</goals>
<configuration>
<args>
<arg>
-dependencyfile
</arg>
<arg>
${project.build.directory}/.scala_dependencies
</arg>
</args>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>
org.apache.maven.plugins
</groupId>
<artifactId>
maven-shade-plugin
</artifactId>
<version>
2.3
</version>
<configuration>
<finalName>
${project.artifactId}-${project.version}
</finalName>
<transformers>
<transformer
implementation=
"org.apache.maven.plugins.shade.resource.ManifestResourceTransformer"
>
<manifestEntries>
<Main-Class>
${app.main.class}
</Main-Class>
<X-Compile-Source-JDK>
${maven.compile.source}
</X-Compile-Source-JDK>
<X-Compile-Target-JDK>
${maven.compile.target}
</X-Compile-Target-JDK>
</manifestEntries>
</transformer>
</transformers>
</configuration>
<executions>
<execution>
<phase>
package
</phase>
<goals>
<goal>
shade
</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
biopet-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecuteble.scala
0 → 100644
View file @
4f6ea975
package
nl.lumc.sasc.biopet.core
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
nl.lumc.sasc.biopet.pipelines.gatk.GatkBenchmarkGenotyping
import
nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping
import
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline
import
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling
import
nl.lumc.sasc.biopet.pipelines.gatk.GatkVcfSampleCompare
import
nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
object
BiopetExecuteble
{
val
pipelines
:
Map
[
String
,
PipelineCommand
]
=
Map
(
"flexiprep"
->
Flexiprep
,
"mapping"
->
Mapping
,
"gentrap"
->
Gentrap
,
"bam-metrics"
->
BamMetrics
,
"gatk-benchmark-genotyping"
->
GatkBenchmarkGenotyping
,
"gatk-genotyping"
->
GatkGenotyping
,
"gatk-variantcalling"
->
GatkVariantcalling
,
"gatk-pipeline"
->
GatkPipeline
,
"gatk-vcf-sample-compare"
->
GatkVcfSampleCompare
)
/**
* @param args the command line arguments
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
if
(
args
.
isEmpty
)
println
(
pipelineList
)
else
if
(
pipelines
.
contains
(
args
.
head
))
pipelines
(
args
.
head
).
main
(
args
.
tail
)
else
{
println
(
"Pipeline '"
+
args
.
head
+
"' does not exist"
)
println
(
pipelineList
)
}
def
pipelineList
:
String
=
{
val
pipelinesArray
=
for
((
k
,
v
)
<-
pipelines
)
yield
k
"Available pipelines:"
+
pipelinesArray
.
mkString
(
"\n- "
,
"\n- "
,
"\n"
)
+
"please suply a pipeline"
}
}
}
flexiprep/nbactions.xml
View file @
4f6ea975
...
...
@@ -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 -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz
-R2 /media/LocalData/test/1k_R2_001.fq.gz
-outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -sample test -library test
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -sample test -library test
-run
</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 -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz
-R2 /media/LocalData/test/1k_R2_001.fq.gz
-outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -sample test -library test
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -sample test -library test
-run
</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 -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz
-R2 /media/LocalData/test/1k_R2_001.fq.gz
-outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -sample test -library test
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R1 /media/LocalData/test/1k_R1_001.tmp.fq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG -sample test -library test
-run
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
mapping/examples/test.json
View file @
4f6ea975
{
"samtools"
:
{
"exe"
:
"test"
},
"star"
:
{
"exe"
:
"test"
},
"reference"
:
"/blabla/blabla.fa"
,
"fastqc"
:
{
"exe"
:
"/home/pjvan_thof/Downloads/FastQC/fastqc"
},
"bwa"
:
{
"exe"
:
"test"
},
...
...
mapping/nbactions.xml
View file @
4f6ea975
...
...
@@ -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 -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
bwa
-l DEBUG -numberChunks
10
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
star
-l DEBUG
-skipmarkduplicates -skipflexiprep -skipmetrics
-numberChunks
2
</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 -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
bwa
-l DEBUG -numberChunks
10
</exec.args>
<exec.args>
-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
star
-l DEBUG
-skipmarkduplicates -skipflexiprep -skipmetrics
-numberChunks
2
</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 -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
bwa
-l DEBUG -numberChunks
10
</exec.args>
<exec.args>
-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R1 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_1.fastq.gz -R2 /data/DIV5/SASC/pjvan_thof/rig_validation/input/gcat_set_025/gcat_set_025_2.fastq.gz -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN
star
-l DEBUG
-skipmarkduplicates -skipflexiprep -skipmetrics
-numberChunks
2
</exec.args>
<exec.executable>
java
</exec.executable>
<exec.workingdir>
/home/pjvan_thof/pipelines/test
</exec.workingdir>
</properties>
...
...
pom.xml
View file @
4f6ea975
...
...
@@ -14,5 +14,6 @@
<module>
bam-metrics
</module>
<module>
pipeline-template
</module>
<module>
gatk
</module>
<module>
biopet-package
</module>
</modules>
</project>
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