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Commit 6f608545 authored by Peter van 't Hof's avatar Peter van 't Hof
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Added single pipeline example

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external-examples/pom.xml 0 → 100644
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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">
<parent>
<artifactId>BiopetRoot</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.5.0-DEV</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<packaging>pom</packaging>
<artifactId>ExternalExamples</artifactId>
<modules>
<module>single-pipeline</module>
</modules>
</project>
\ No newline at end of file
external-examples/single-pipeline/.gitignore 0 → 100644
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# Project-related
dependency-reduced-pom.xml
git.properties
# gedit
*~
# Vim
*.swp
# IntelliJ
.idea/*
*.iml
target/
public/target/
protected/target/
external-examples/single-pipeline/README.md 0 → 100644
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Test implementation of Magpie 2.0
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external-examples/single-pipeline/pom.xml 0 → 100644
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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>
<groupId>nl.lumc.kg</groupId>
<artifactId>SinglePipeline</artifactId>
<version>0.5.0-DEV</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<scoverage.plugin.version>1.0.4</scoverage.plugin.version>
<sting.shade.phase>package</sting.shade.phase>
<app.main.class>org.example.group.SinglePipeline</app.main.class>
</properties>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Shiva</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>${basedir}/src/main/scala</sourceDirectory>
<testSourceDirectory>${basedir}/src/test/scala</testSourceDirectory>
<testResources>
<testResource>
<directory>${basedir}/src/test/resources</directory>
<includes>
<include>**/*</include>
</includes>
</testResource>
</testResources>
<resources>
<resource>
<directory>${basedir}/src/main/resources</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.1</version>
<configuration>
<!--suppress MavenModelInspection -->
<finalName>Magpie-${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>
<!--suppress MavenModelInspection -->
<X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
<!--suppress MavenModelInspection -->
<X-Compile-Target-JDK>${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>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.18.1</version>
<configuration>
<forkCount>1C</forkCount>
<workingDirectory>${project.build.directory}</workingDirectory>
</configuration>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.10</version>
<executions>
<execution>
<id>copy-installed</id>
<phase>prepare-package</phase>
<goals>
<goal>list</goal>
</goals>
<configuration>
<outputFile>${project.build.outputDirectory}/dependency_list.txt</outputFile>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.2.0</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>
<!-- ... (see other usage or goals for details) ... -->
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.5</version>
<executions>
<execution>
<goals>
<goal>test-jar</goal>
</goals>
</execution>
</executions>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<showDeprecation>true</showDeprecation>
</configuration>
</plugin>
<plugin>
<groupId>org.scalariform</groupId>
<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>
</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>
<gitDescribe>
<skip>false</skip>
<always>false</always>
<abbrev>8</abbrev>
<dirty>-dirty</dirty>
<forceLongFormat>false</forceLongFormat>
</gitDescribe>
</configuration>
</plugin>
<plugin>
<groupId>com.mycila</groupId>
<artifactId>license-maven-plugin</artifactId>
<version>2.6</version>
<configuration>
<excludes>
<exclude>**/*git*</exclude>
<exclude>**/License*</exclude>
<exclude>**/*.bam</exclude>
<exclude>**/*.bai</exclude>
<exclude>**/*.gtf</exclude>
<exclude>**/*.fq</exclude>
<exclude>**/*.sam</exclude>
<exclude>**/*.bed</exclude>
<exclude>**/*.refFlat</exclude>
<exclude>**/*.R</exclude>
<exclude>**/*.rscript</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.scoverage</groupId>
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
<configuration>
<scalaVersion>2.10.2</scalaVersion>
<!-- other parameters -->
</configuration>
</plugin>
</plugins>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.scoverage</groupId>
<artifactId>scoverage-maven-plugin</artifactId>
<version>${scoverage.plugin.version}</version>
</plugin>
</plugins>
</reporting>
</project>
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external-examples/single-pipeline/src/main/scala/org/example/group/SinglePipeline.scala 0 → 100644
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package org.example.group
import nl.lumc.sasc.biopet.core.PipelineCommand
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 8/28/15.
*/
class SinglePipeline(val root: Configurable) extends QScript with SummaryQScript {
def this() = this(null)
def summaryFile = new File(outputDir, "magpie.summary.json")
def summaryFiles: Map[String, File] = Map()
def summarySettings = Map()
def init(): Unit = {
}
def biopetScript: Unit = {
val shiva = new Shiva(this)
shiva.init()
shiva.biopetScript()
addAll(shiva.functions)
addSummaryQScript(shiva)
}
}
object SinglePipeline extends PipelineCommand
pom.xml
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......@@ -16,5 +16,6 @@
<modules>
<module>public</module>
<module>protected</module>
<module>external-examples</module>
</modules>
</project>
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