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biopet.biopet
Commit 34023585 authored by Peter van 't Hof's avatar Peter van 't Hof
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Separate framework from packaging

parent 7d730675
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Showing with 162 additions and 73 deletions
.gitignore
View file @ 34023585
# Project-related
dependency-reduced-pom.xml
/biopet-framework/src/main/resources/git.properties
git.properties
# gedit
*~
......
public/biopet-framework/pom.xml
View file @ 34023585
......@@ -117,65 +117,6 @@
</resource>
</resources>
<plugins>
<plugin>
<groupId>com.mycila</groupId>
<artifactId>license-maven-plugin</artifactId>
<version>2.6</version>
<configuration>
<header>nl/lumc/sasc/biopet/License.txt</header>
<properties>
<owner>Leiden University Medical Center - Sequencing Analysis Support Core</owner>
<email>sasc@lumc.nl</email>
</properties>
<excludes>
<exclude>**/README</exclude>
<exclude>src/test/resources/**</exclude>
<exclude>src/main/resources/**</exclude>
<exclude>src/main/scripts/**</exclude>
</excludes>
</configuration>
<executions>
<execution>
<goals>
<goal>check</goal>
</goals>
</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>
<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>
......@@ -211,7 +152,7 @@
</archive>
</configuration>
</plugin>
<plugin>
<!-- <plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
......@@ -227,7 +168,7 @@
</transformer>
</transformers>
<filters>
<!-- <filter>
<filter>
<artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
<includes>
<include>*/**</include>
......@@ -245,7 +186,7 @@
<include>org/apache/**</include>
<include>scala/tools/nsc/reporters/**</include>
</includes>
</filter>-->
</filter>
</filters>
</configuration>
<executions>
......@@ -256,7 +197,7 @@
</goals>
</execution>
</executions>
</plugin>
</plugin>-->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
......
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
View file @ 34023585
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.core
import java.util.Properties
import org.apache.log4j.Logger
object BiopetExecutable extends Logging {
trait BiopetExecutable extends Logging {
val pipelines: List[MainCommand] = List(
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep,
......@@ -107,15 +107,9 @@ object BiopetExecutable extends Logging {
}
}
def getVersion = {
getClass.getPackage.getImplementationVersion + " (" + getCommitHash + ")"
}
def getVersion = BiopetExecutable.getVersion
def getCommitHash = {
val prop = new Properties()
prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))
prop.getProperty("git.commit.id.abbrev")
}
def getCommitHash = BiopetExecutable.getCommitHash
def checkDirtyBuild(logger: Logger) {
val prop = new Properties()
......@@ -130,3 +124,15 @@ object BiopetExecutable extends Logging {
}
checkDirtyBuild(logger)
}
object BiopetExecutable {
def getVersion = {
getClass.getPackage.getImplementationVersion + " (" + getCommitHash + ")"
}
def getCommitHash = {
val prop = new Properties()
prop.load(getClass.getClassLoader.getResourceAsStream("git.properties"))
prop.getProperty("git.commit.id.abbrev")
}
}
\ No newline at end of file
public/biopet-public-package/.gitignore 0 → 100644
View file @ 34023585
/target/
\ No newline at end of file
public/biopet-public-package/pom.xml 0 → 100644
View file @ 34023585
<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>BiopetPublicPackage</artifactId>
<version>0.2.0-DEV</version>
<packaging>jar</packaging>
<inceptionYear>2014</inceptionYear>
<name>BiopetPublicPackage</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.BiopetExecutablePublic</app.main.class>
</properties>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetFramework</artifactId>
<version>0.2.0-DEV</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>src/main/resources</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>
<arg>-deprecation</arg>
<arg>-feature</arg>
</args>
</configuration>
</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>
<useNativeGit>true</useNativeGit>
<dotGitDirectory>${project.basedir}/../../.git</dotGitDirectory>
<skipPoms>false</skipPoms>
<generateGitPropertiesFile>true</generateGitPropertiesFile>
<generateGitPropertiesFilename>src/main/resources/git.properties</generateGitPropertiesFilename>
<failOnNoGitDirectory>false</failOnNoGitDirectory>
<abbrevLength>7</abbrevLength>
<skip>false</skip>
<excludeProperties></excludeProperties>
<gitDescribe>
<skip>false</skip>
<always>false</always>
<abbrev>7</abbrev>
<dirty>-dirty</dirty>
<forceLongFormat>false</forceLongFormat>
</gitDescribe>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.5</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.3</version>
<configuration>
<finalName>Biopet-${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>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala 0 → 100644
View file @ 34023585
package nl.lumc.sasc.biopet.core
object BiopetExecutablePublic extends BiopetExecutable
public/pom.xml
View file @ 34023585
......@@ -13,5 +13,6 @@
</properties>
<modules>
<module>biopet-framework</module>
<module>biopet-public-package</module>
</modules>
</project>
\ No newline at end of file
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