Commit c6f4c405 authored by bow's avatar bow
Browse files

Merge branch 'feature-licence' into 'develop'

Feature licence

Switch so separated poms because of license issue

See merge request !58
parents f12c5edf 44bf4593
/target/
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<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>BiopetGatkPipelines</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.2.0-DEV</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>BiopetGatkPipelines</name>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatkExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
/target/
\ No newline at end of file
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetProtectedPackage</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.2.0-DEV</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>BiopetProtectedPackage</name>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetPublicPackage</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatkPipelines</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Basty</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<configuration>
<finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${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>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
package nl.lumc.sasc.biopet.core
object BiopetExecutableProtected extends BiopetExecutable {
def pipelines: List[MainCommand] = BiopetExecutablePublic.pipelines ::: List(
nl.lumc.sasc.biopet.pipelines.gatk.GatkBenchmarkGenotyping,
nl.lumc.sasc.biopet.pipelines.gatk.GatkGenotyping,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantcalling,
nl.lumc.sasc.biopet.pipelines.gatk.GatkPipeline,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVariantRecalibration,
nl.lumc.sasc.biopet.pipelines.gatk.GatkVcfSampleCompare,
nl.lumc.sasc.biopet.pipelines.basty.Basty)
def tools = BiopetExecutablePublic.tools
}
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<?xml version="1.0" encoding="UTF-8"?>
<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>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetRoot</artifactId>
<version>0.2.0-DEV</version>
<relativePath>../</relativePath>
</parent>
<artifactId>BiopetGatk</artifactId>
<name>BiopetGatk</name>
<packaging>pom</packaging>
<modules>
<module>biopet-gatk-extensions</module>
<module>biopet-gatk-pipelines</module>
<module>basty</module>
<module>biopet-protected-package</module>
</modules>
</project>
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*.bam binary
*.bam.bai binary
# Project-related
dependency-reduced-pom.xml
git.properties
# gedit
*~
# Vim
*.swp
# IntelliJ
.idea/workspace.xml
/target/
/public/target/
/protected/target/
/target/
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