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Commit 4557807c authored by Peter van 't Hof's avatar Peter van 't Hof
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Merge commit 'cfae9015' 

Conflicts:
	flexiprep/nbactions.xml
	gatk/gatk-pipeline/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
	gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
	mapping/examples/test.json
	mapping/nbactions.xml
	pom.xml
parent 4f6ea975
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bam-metrics/.gitignore deleted 100644 → 0
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/target/
\ No newline at end of file
bam-metrics/nbactions.xml deleted 100644 → 0
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.pipelines.bammetrics.BamMetrics -BAM test.bam -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/bam-metrics/examples/test.json</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.pipelines.bammetrics.BamMetrics -BAM test.bam -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/bam-metrics/examples/test.json</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.pipelines.bammetrics.BamMetrics -BAM test.bam -outDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/bam-metrics/examples/test.json</exec.args>
<exec.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties>
</action>
</actions>
bam-metrics/pom.xml deleted 100644 → 0
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>Bam-Metrics</artifactId>
<version>0.1.3</version>
<packaging>jar</packaging>
<name>Bam-Metrics</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.bammetrics.BamMetrics</app.main.class>
</properties>
<dependencies>
<!-- <dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>-->
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-compiler</artifactId>
<version>2.11.0</version>
</dependency>
<!-- <dependency>
<groupId>org.utgenome.thirdparty</groupId>
<artifactId>picard</artifactId>
<version>1.86.0</version>
</dependency>-->
<!-- <dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.9.2</artifactId>
<version>2.0.M4</version>
<scope>test</scope>
</dependency>-->
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet-Framework</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-surefire-plugin</artifactId>
<version>2.7.2</version>
<executions>
<execution>
<id>default-test</id>
Disable the default-test by putting it in phase none
<phase>none</phase>
</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>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
<exclude>org.scala-lang:scala-reflect</exclude>
<exclude>org.scala-lang.modules:*</exclude>
</excludes>
</artifactSet>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
mapping/examples/test.json → biopet-framework/examples/mapping.json
View file @ 4557807c
{
"samtools": {"exe": "test"},
"star": {"exe": "test"},
"reference": "/blabla/blabla.fa",
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"bwa": { "exe": "test" },
......
biopet-framework/pom.xml
View file @ 4557807c
......@@ -3,26 +3,19 @@
<modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet-Framework</artifactId>
<artifactId>Biopet</artifactId>
<version>0.1.3</version>
<packaging>jar</packaging>
<name>Biopet-Framework</name>
<name>Biopet</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>
<sting.binary-dist.name>SASC-Pipelines</sting.binary-dist.name>
<app.main.class>org.broadinstitute.gatk.queue.QCommandLine</app.main.class>
<app.main.class>nl.lumc.sasc.biopet.core.BiopetExecutable</app.main.class>
</properties>
<dependencies>
......@@ -32,23 +25,11 @@
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-compiler</artifactId>
<version>2.11.0</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.11.0</version>
<version>2.11.2</version>
</dependency>
<!-- <dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.9.2</artifactId>
<version>2.0.M4</version>
<scope>test</scope>
</dependency>-->
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue-package-distribution</artifactId>
......@@ -57,10 +38,18 @@
<dependency>
<groupId>io.argonaut</groupId>
<artifactId>argonaut_2.11</artifactId>
<version>6.1-M3</version>
<version>6.1-M4</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/scripts</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.scala-tools</groupId>
......@@ -83,68 +72,47 @@
</execution>
</executions>
</plugin>
<!-- <plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.7.2</version>
<executions>
<execution>
<id>default-test</id>
Disable the default-test by putting it in phase none
<phase>none</phase>
</execution>
</executions>
</plugin>-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<configuration>
<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>
<artifactSet>
<excludes>
<exclude>junit:junit</exclude>
<!-- <exclude>org.scala-lang:scala-compiler</exclude>-->
<!-- <exclude>org.scala-lang:scala-library</exclude>-->
<exclude>org.scala-lang:scala-reflect</exclude>
<exclude>org.scala-lang.modules:*</exclude>
</excludes>
</artifactSet>
<filters>
<filter>
<artifact>org.scala-lang:scala-compiler</artifact>
<includes>
<include>scala/tools/nsc/reporters/**</include>
</includes>
</filter>
<filter>
<artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
<excludes>
<!-- <exclude>scala/**</exclude>-->
</excludes>
<includes>
<include>*/**</include>
</includes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<configuration>
<finalName>${project.artifactId}</finalName>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${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>
<filters>
<filter>
<artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
<includes>
<include>picard/**</include>
<include>htsjdk/**</include>
<include>javassist/**</include>
<include>com/google/**</include>
<include>org/reflections/</include>
<include>org/jgrapht/**</include>
<include>org/broadinstitute/**</include>
<include>org/apache/**</include>
<include>scala/tools/nsc/reporters/**</include>
</includes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala 0 → 100644
View file @ 4557807c
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 BiopetExecutable {
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) {
System.err.println(pipelineList)
System.exit(1)
}
else if (pipelines.contains(args.head)) pipelines(args.head).main(args.tail)
else {
System.err.println("Pipeline '" + args.head + "' does not exist")
System.err.println(pipelineList)
System.exit(1)
}
def pipelineList: String = {
val pipelinesArray = for ((k,v) <- pipelines) yield k
"Available pipelines:" + pipelinesArray.mkString("\n- ", "\n- ", "\n") + "please supply a valid pipeline"
}
}
}
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