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
<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">
<?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>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<name>Biopet</name>
<packaging>pom</packaging>
<version>0.2.0-DEV</version>
<packaging>jar</packaging>
<name>BiopetFramework</name>
<url>http://maven.apache.org</url>
<modules>
<module>biopet-framework</module>
<module>biopet-public-package</module>
<module>bammetrics</module>
<module>flexiprep</module>
<module>gentrap</module>
<module>mapping</module>
<module>sage</module>
<module>yamsvp</module>
</modules>
<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.core.BiopetExecutable</app.main.class>
</properties>
<repositories>
<repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.9.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.11</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.11.2</version>
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.3</version>
</dependency>
<dependency>
<groupId>io.argonaut</groupId>
<artifactId>argonaut_2.11</artifactId>
<version>6.1-M4</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-core</artifactId>
<version>3.1.0</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava3-sequencing</artifactId>
<version>3.1.0</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>18.0</version>
</dependency>
<dependency>
<groupId>com.github.scopt</groupId>
<artifactId>scopt_2.10</artifactId>
<version>3.2.0</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/scripts</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<includes>
......@@ -95,40 +32,6 @@
</resource>
</resources>
<plugins>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>2.1.10</version>
<executions>
<execution>
<goals>
<goal>revision</goal>
</goals>
</execution>
</executions>
<configuration>
<prefix>git</prefix>
<dateFormat>dd.MM.yyyy '@' HH:mm:ss z</dateFormat>
<verbose>false</verbose>
<useNativeGit>true</useNativeGit>
<dotGitDirectory>${project.basedir}/../.git</dotGitDirectory>
<skipPoms>false</skipPoms>
<generateGitPropertiesFile>true</generateGitPropertiesFile>
<generateGitPropertiesFilename>src/main/resources/git.properties</generateGitPropertiesFilename>
<failOnNoGitDirectory>false</failOnNoGitDirectory>
<abbrevLength>7</abbrevLength>
<skip>false</skip>
<excludeProperties></excludeProperties>
<gitDescribe>
<skip>false</skip>
<always>false</always>
<abbrev>7</abbrev>
<dirty>-dirty</dirty>
<forceLongFormat>false</forceLongFormat>
</gitDescribe>
</configuration>
</plugin>
<plugin>
<groupId>org.scala-tools</groupId>
<artifactId>maven-scala-plugin</artifactId>
......@@ -164,52 +67,6 @@
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<configuration>
<finalName>Biopet-${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>
<filter>
<artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
<includes>
<include>*/**</include>
<include>org/simpleframework/**</include>
<include>org/jets3t/**</include>
<include>com/sun/**</include>
<include>org/ggf/**</include>
<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>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
......@@ -254,6 +111,39 @@
</execution>
</executions>
</plugin>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>2.1.10</version>
<executions>
<execution>
<goals>
<goal>revision</goal>
</goals>
</execution>
</executions>
<configuration>
<prefix>git</prefix>
<dateFormat>dd.MM.yyyy '@' HH:mm:ss z</dateFormat>
<verbose>false</verbose>
<dotGitDirectory>${basedir}/../../.git</dotGitDirectory>
<useNativeGit>true</useNativeGit>
<skipPoms>false</skipPoms>
<generateGitPropertiesFile>true</generateGitPropertiesFile>
<generateGitPropertiesFilename>src/main/resources/git.properties</generateGitPropertiesFilename>
<failOnNoGitDirectory>false</failOnNoGitDirectory>
<abbrevLength>8</abbrevLength>
<skip>false</skip>
<excludeProperties></excludeProperties>
<gitDescribe>
<skip>false</skip>
<always>false</always>
<abbrev>8</abbrev>
<dirty>-dirty</dirty>
<forceLongFormat>false</forceLongFormat>
</gitDescribe>
</configuration>
</plugin>
</plugins>
</build>
</project>
</project>
\ No newline at end of file
/target/
\ No newline at end of file
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Sage</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.2.0-DEV</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>Sage</name>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
/target/
\ No newline at end of file
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Yamsvp</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.2.0-DEV</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>Yamsvp</name>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
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