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Commit 14790fa3 authored by Peter van 't Hof's avatar Peter van 't Hof
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Merge branch 'feature-pom_updates' into 'develop' 

Feature pom updates

See commits :).

See merge request !29
parents 2c360e07 3bfe38c5
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biopet-framework/pom.xml
+ 101
− 99
View file @ 14790fa3
<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>
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>BiopetFramework</artifactId>
<version>0.2.0-DEV</version>
<packaging>jar</packaging>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<version>0.2.0-DEV</version>
<packaging>jar</packaging>
<name>BiopetFramework</name>
<url>http://maven.apache.org</url>
<name>BiopetFramework</name>
<url>http://maven.apache.org</url>
<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>
<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>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>
<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>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
......@@ -68,9 +67,9 @@
<version>18.0</version>
</dependency>
<dependency>
<groupId>com.github.scopt</groupId>
<artifactId>scopt_2.10</artifactId>
<version>3.2.0</version>
<groupId>com.github.scopt</groupId>
<artifactId>scopt_2.10</artifactId>
<version>3.2.0</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
......@@ -81,16 +80,16 @@
<build>
<resources>
<resource>
<directory>src/main/scripts</directory>
<includes>
<include>**/*</include>
</includes>
<directory>src/main/scripts</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
<resource>
<directory>src/main/resources</directory>
<includes>
<include>**/*</include>
</includes>
<directory>src/main/resources</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
</resources>
<plugins>
......@@ -102,7 +101,7 @@
<execution>
<goals>
<goal>revision</goal>
</goals>
</goals>
</execution>
</executions>
......@@ -141,9 +140,10 @@
</goals>
<configuration>
<args>
<!-- <arg>-make:transitive</arg>-->
<arg>-dependencyfile</arg>
<arg>${project.build.directory}/.scala_dependencies</arg>
<arg>-deprecation</arg>
<arg>-feature</arg>
</args>
</configuration>
</execution>
......@@ -154,7 +154,7 @@
<artifactId>maven-jar-plugin</artifactId>
<version>2.5</version>
<configuration>
<archive>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
......@@ -163,50 +163,50 @@
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<configuration>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<configuration>
<finalName>Biopet-${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>
<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>
<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>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
......@@ -221,33 +221,35 @@
<artifactId>scalariform-maven-plugin</artifactId>
<version>0.1.4</version>
<executions>
<execution>
<phase>process-sources</phase>
<goals>
<goal>format</goal>
</goals>
<configuration>
<rewriteArrowSymbols>false</rewriteArrowSymbols>
<alignParameters>true</alignParameters>
<alignSingleLineCaseStatements_maxArrowIndent>40</alignSingleLineCaseStatements_maxArrowIndent>
<alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
<compactStringConcatenation>false</compactStringConcatenation>
<compactControlReadability>false</compactControlReadability>
<doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
<formatXml>true</formatXml>
<indentLocalDefs>false</indentLocalDefs>
<indentPackageBlocks>true</indentPackageBlocks>
<indentSpaces>2</indentSpaces>
<placeScaladocAsterisksBeneathSecondAsterisk>false</placeScaladocAsterisksBeneathSecondAsterisk>
<preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
<preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
<rewriteArrowSymbols>false</rewriteArrowSymbols>
<spaceBeforeColon>false</spaceBeforeColon>
<spaceInsideBrackets>false</spaceInsideBrackets>
<spaceInsideParentheses>false</spaceInsideParentheses>
<spacesWithinPatternBinders>true</spacesWithinPatternBinders>
</configuration>
</execution>
<execution>
<phase>process-sources</phase>
<goals>
<goal>format</goal>
</goals>
<configuration>
<rewriteArrowSymbols>false</rewriteArrowSymbols>
<alignParameters>true</alignParameters>
<alignSingleLineCaseStatements_maxArrowIndent>40
</alignSingleLineCaseStatements_maxArrowIndent>
<alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
<compactStringConcatenation>false</compactStringConcatenation>
<compactControlReadability>false</compactControlReadability>
<doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
<formatXml>true</formatXml>
<indentLocalDefs>false</indentLocalDefs>
<indentPackageBlocks>true</indentPackageBlocks>
<indentSpaces>2</indentSpaces>
<placeScaladocAsterisksBeneathSecondAsterisk>false
</placeScaladocAsterisksBeneathSecondAsterisk>
<preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
<preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
<rewriteArrowSymbols>false</rewriteArrowSymbols>
<spaceBeforeColon>false</spaceBeforeColon>
<spaceInsideBrackets>false</spaceInsideBrackets>
<spaceInsideParentheses>false</spaceInsideParentheses>
<spacesWithinPatternBinders>true</spacesWithinPatternBinders>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
......
pom.xml
+ 11
− 10
View file @ 14790fa3
<?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>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.1.3</version>
<packaging>pom</packaging>
<name>Biopet</name>
<modules>
<module>biopet-framework</module>
</modules>
<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>Biopet</artifactId>
<version>0.2.0-DEV</version>
<packaging>pom</packaging>
<name>Biopet</name>
<modules>
<module>biopet-framework</module>
</modules>
</project>
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