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biopet.biopet
Commit 4f6ea975 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added BiopetPackage as complete package

parent 33b1e8fc
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Showing with 249 additions and 6 deletions
.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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