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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" <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"> 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> <modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId> <artifactId>BiopetFramework</artifactId>
<version>0.2.0-DEV</version> <version>0.2.0-DEV</version>
<packaging>jar</packaging> <packaging>jar</packaging>
<name>BiopetFramework</name> <name>BiopetFramework</name>
<url>http://maven.apache.org</url> <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> <repositories>
<repository> <repository>
<id>biojava-maven-repo</id> <id>biojava-maven-repo</id>
<name>BioJava repository</name> <name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url> <url>http://www.biojava.org/download/maven/</url>
</repository> </repository>
</repositories> </repositories>
<dependencies> <dependencies>
<dependency> <dependency>
<groupId>org.testng</groupId> <groupId>org.testng</groupId>
<artifactId>testng</artifactId> <artifactId>testng</artifactId>
<version>6.8</version> <version>6.8</version>
<scope>test</scope> <scope>test</scope>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.scalatest</groupId> <groupId>org.scalatest</groupId>
...@@ -68,9 +67,9 @@ ...@@ -68,9 +67,9 @@
<version>18.0</version> <version>18.0</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.github.scopt</groupId> <groupId>com.github.scopt</groupId>
<artifactId>scopt_2.10</artifactId> <artifactId>scopt_2.10</artifactId>
<version>3.2.0</version> <version>3.2.0</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.mockito</groupId> <groupId>org.mockito</groupId>
...@@ -81,16 +80,16 @@ ...@@ -81,16 +80,16 @@
<build> <build>
<resources> <resources>
<resource> <resource>
<directory>src/main/scripts</directory> <directory>src/main/scripts</directory>
<includes> <includes>
<include>**/*</include> <include>**/*</include>
</includes> </includes>
</resource> </resource>
<resource> <resource>
<directory>src/main/resources</directory> <directory>src/main/resources</directory>
<includes> <includes>
<include>**/*</include> <include>**/*</include>
</includes> </includes>
</resource> </resource>
</resources> </resources>
<plugins> <plugins>
...@@ -102,7 +101,7 @@ ...@@ -102,7 +101,7 @@
<execution> <execution>
<goals> <goals>
<goal>revision</goal> <goal>revision</goal>
</goals> </goals>
</execution> </execution>
</executions> </executions>
...@@ -141,9 +140,10 @@ ...@@ -141,9 +140,10 @@
</goals> </goals>
<configuration> <configuration>
<args> <args>
<!-- <arg>-make:transitive</arg>-->
<arg>-dependencyfile</arg> <arg>-dependencyfile</arg>
<arg>${project.build.directory}/.scala_dependencies</arg> <arg>${project.build.directory}/.scala_dependencies</arg>
<arg>-deprecation</arg>
<arg>-feature</arg>
</args> </args>
</configuration> </configuration>
</execution> </execution>
...@@ -154,7 +154,7 @@ ...@@ -154,7 +154,7 @@
<artifactId>maven-jar-plugin</artifactId> <artifactId>maven-jar-plugin</artifactId>
<version>2.5</version> <version>2.5</version>
<configuration> <configuration>
<archive> <archive>
<manifest> <manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries> <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries> <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
...@@ -163,50 +163,50 @@ ...@@ -163,50 +163,50 @@
</configuration> </configuration>
</plugin> </plugin>
<plugin> <plugin>
<groupId>org.apache.maven.plugins</groupId> <groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId> <artifactId>maven-shade-plugin</artifactId>
<version>2.3</version> <version>2.3</version>
<configuration> <configuration>
<finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName> <finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName>
<transformers> <transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer"> <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries> <manifestEntries>
<Main-Class>${app.main.class}</Main-Class> <Main-Class>${app.main.class}</Main-Class>
<X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK> <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
<X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK> <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
</manifestEntries> </manifestEntries>
</transformer> </transformer>
</transformers> </transformers>
<filters> <filters>
<filter> <filter>
<artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact> <artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
<includes> <includes>
<include>*/**</include> <include>*/**</include>
<include>org/simpleframework/**</include> <include>org/simpleframework/**</include>
<include>org/jets3t/**</include> <include>org/jets3t/**</include>
<include>com/sun/**</include> <include>com/sun/**</include>
<include>org/ggf/**</include> <include>org/ggf/**</include>
<include>picard/**</include> <include>picard/**</include>
<include>htsjdk/**</include> <include>htsjdk/**</include>
<include>javassist/**</include> <include>javassist/**</include>
<include>com/google/**</include> <include>com/google/**</include>
<include>org/reflections/</include> <include>org/reflections/</include>
<include>org/jgrapht/**</include> <include>org/jgrapht/**</include>
<include>org/broadinstitute/**</include> <include>org/broadinstitute/**</include>
<include>org/apache/**</include> <include>org/apache/**</include>
<include>scala/tools/nsc/reporters/**</include> <include>scala/tools/nsc/reporters/**</include>
</includes> </includes>
</filter> </filter>
</filters> </filters>
</configuration> </configuration>
<executions> <executions>
<execution> <execution>
<phase>package</phase> <phase>package</phase>
<goals> <goals>
<goal>shade</goal> <goal>shade</goal>
</goals> </goals>
</execution> </execution>
</executions> </executions>
</plugin> </plugin>
<plugin> <plugin>
<groupId>org.apache.maven.plugins</groupId> <groupId>org.apache.maven.plugins</groupId>
...@@ -221,33 +221,35 @@ ...@@ -221,33 +221,35 @@
<artifactId>scalariform-maven-plugin</artifactId> <artifactId>scalariform-maven-plugin</artifactId>
<version>0.1.4</version> <version>0.1.4</version>
<executions> <executions>
<execution> <execution>
<phase>process-sources</phase> <phase>process-sources</phase>
<goals> <goals>
<goal>format</goal> <goal>format</goal>
</goals> </goals>
<configuration> <configuration>
<rewriteArrowSymbols>false</rewriteArrowSymbols> <rewriteArrowSymbols>false</rewriteArrowSymbols>
<alignParameters>true</alignParameters> <alignParameters>true</alignParameters>
<alignSingleLineCaseStatements_maxArrowIndent>40</alignSingleLineCaseStatements_maxArrowIndent> <alignSingleLineCaseStatements_maxArrowIndent>40
<alignSingleLineCaseStatements>true</alignSingleLineCaseStatements> </alignSingleLineCaseStatements_maxArrowIndent>
<compactStringConcatenation>false</compactStringConcatenation> <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
<compactControlReadability>false</compactControlReadability> <compactStringConcatenation>false</compactStringConcatenation>
<doubleIndentClassDeclaration>false</doubleIndentClassDeclaration> <compactControlReadability>false</compactControlReadability>
<formatXml>true</formatXml> <doubleIndentClassDeclaration>false</doubleIndentClassDeclaration>
<indentLocalDefs>false</indentLocalDefs> <formatXml>true</formatXml>
<indentPackageBlocks>true</indentPackageBlocks> <indentLocalDefs>false</indentLocalDefs>
<indentSpaces>2</indentSpaces> <indentPackageBlocks>true</indentPackageBlocks>
<placeScaladocAsterisksBeneathSecondAsterisk>false</placeScaladocAsterisksBeneathSecondAsterisk> <indentSpaces>2</indentSpaces>
<preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis> <placeScaladocAsterisksBeneathSecondAsterisk>false
<preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments> </placeScaladocAsterisksBeneathSecondAsterisk>
<rewriteArrowSymbols>false</rewriteArrowSymbols> <preserveDanglingCloseParenthesis>true</preserveDanglingCloseParenthesis>
<spaceBeforeColon>false</spaceBeforeColon> <preserveSpaceBeforeArguments>false</preserveSpaceBeforeArguments>
<spaceInsideBrackets>false</spaceInsideBrackets> <rewriteArrowSymbols>false</rewriteArrowSymbols>
<spaceInsideParentheses>false</spaceInsideParentheses> <spaceBeforeColon>false</spaceBeforeColon>
<spacesWithinPatternBinders>true</spacesWithinPatternBinders> <spaceInsideBrackets>false</spaceInsideBrackets>
</configuration> <spaceInsideParentheses>false</spaceInsideParentheses>
</execution> <spacesWithinPatternBinders>true</spacesWithinPatternBinders>
</configuration>
</execution>
</executions> </executions>
</plugin> </plugin>
</plugins> </plugins>
......
pom.xml
+ 11
− 10
View file @ 14790fa3
<?xml version="1.0" encoding="UTF-8"?> <?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"> <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
<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">
<groupId>nl.lumc.sasc</groupId> <modelVersion>4.0.0</modelVersion>
<artifactId>Biopet</artifactId> <groupId>nl.lumc.sasc</groupId>
<version>0.1.3</version> <artifactId>Biopet</artifactId>
<packaging>pom</packaging> <version>0.2.0-DEV</version>
<name>Biopet</name> <packaging>pom</packaging>
<modules> <name>Biopet</name>
<module>biopet-framework</module> <modules>
</modules> <module>biopet-framework</module>
</modules>
</project> </project>
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