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Mirrors
biopet.biopet
Commits
e07befed
Commit
e07befed
authored
Nov 24, 2014
by
Peter van 't Hof
Browse files
now works with parent poms
parent
e51c2232
Changes
17
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Inline
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.gitignore
View file @
e07befed
...
...
@@ -8,3 +8,6 @@ git.properties
*.swp
# IntelliJ
.idea/workspace.xml
/target/
/public/target/
/protected/target/
\ No newline at end of file
pom.xml
View file @
e07befed
...
...
@@ -11,4 +11,106 @@
<module>
public
</module>
<module>
protected
</module>
</modules>
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
</properties>
<build>
<resources>
<resource>
<directory>
src/main/scripts
</directory>
<includes>
<include>
**/*
</include>
</includes>
</resource>
<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>
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-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>
</plugins>
</build>
</project>
protected/basty/pom.xml
View file @
e07befed
...
...
@@ -4,19 +4,17 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Basty
</artifactId>
<version>
0.2.0-DEV
</version>
<packaging>
jar
</packaging>
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatk
</artifactId>
<version>
0.2.0-DEV
</version>
<relativePath>
../
</relativePath>
</parent>
<inceptionYear>
2014
</inceptionYear>
<name>
Basty
</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>
<dependencies>
<dependency>
...
...
@@ -35,59 +33,4 @@
<version>
${project.version}
</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>
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-compiler-plugin
</artifactId>
<version>
2.3.2
</version>
<configuration>
<showDeprecation>
true
</showDeprecation>
</configuration>
</plugin>
</plugins>
</build>
</project>
protected/biopet-gatk-extensions/pom.xml
View file @
e07befed
...
...
@@ -4,19 +4,17 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatkExtensions
</artifactId>
<version>
0.2.0-DEV
</version>
<packaging>
jar
</packaging>
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatk
</artifactId>
<version>
0.2.0-DEV
</version>
<relativePath>
../
</relativePath>
</parent>
<inceptionYear>
2014
</inceptionYear>
<name>
BiopetGatkExtensions
</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>
<dependencies>
<dependency>
...
...
@@ -30,59 +28,4 @@
<version>
3.3
</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>
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-compiler-plugin
</artifactId>
<version>
2.3.2
</version>
<configuration>
<showDeprecation>
true
</showDeprecation>
</configuration>
</plugin>
</plugins>
</build>
</project>
protected/biopet-gatk-pipelines/pom.xml
View file @
e07befed
...
...
@@ -4,19 +4,17 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatkPipelines
</artifactId>
<version>
0.2.0-DEV
</version>
<packaging>
jar
</packaging>
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatk
</artifactId>
<version>
0.2.0-DEV
</version>
<relativePath>
../
</relativePath>
</parent>
<inceptionYear>
2014
</inceptionYear>
<name>
BiopetGatkPipelines
</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>
<dependencies>
<dependency>
...
...
@@ -35,59 +33,4 @@
<version>
${project.version}
</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>
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-compiler-plugin
</artifactId>
<version>
2.3.2
</version>
<configuration>
<showDeprecation>
true
</showDeprecation>
</configuration>
</plugin>
</plugins>
</build>
</project>
protected/biopet-protected-package/pom.xml
View file @
e07befed
...
...
@@ -4,20 +4,17 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetProtectedPackage
</artifactId>
<version>
0.2.0-DEV
</version>
<packaging>
jar
</packaging>
<parent>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatk
</artifactId>
<version>
0.2.0-DEV
</version>
<relativePath>
../
</relativePath>
</parent>
<inceptionYear>
2014
</inceptionYear>
<name>
BiopetProtectedPackage
</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.BiopetExecutableProtected
</app.main.class>
</properties>
<dependencies>
<dependency>
...
...
@@ -42,84 +39,7 @@
</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>
...
...
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
View file @
e07befed
...
...
@@ -9,6 +9,6 @@ object BiopetExecutableProtected extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVariantRecalibration
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVcfSampleCompare
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
)
def
tools
=
BiopetExecutablePublic
.
tools
}
\ No newline at end of file
protected/pom.xml
View file @
e07befed
...
...
@@ -16,7 +16,4 @@
<module>
basty
</module>
<module>
biopet-protected-package
</module>
</modules>
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
</properties>
</project>
\ No newline at end of file
public/bammetrics/pom.xml
View file @
e07befed
...
...
@@ -4,19 +4,17 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BamMetrics
</artifactId>
<version>
0.2.0-DEV
</version>
<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>
BamMetrics
</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>
<dependencies>
<dependency>
...
...
@@ -25,59 +23,4 @@
<version>
${project.version}
</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>
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-compiler-plugin
</artifactId>
<version>
2.3.2
</version>
<configuration>
<showDeprecation>
true
</showDeprecation>
</configuration>
</plugin>
</plugins>
</build>
</project>
public/biopet-framework/pom.xml
View file @
e07befed
...
...
@@ -4,19 +4,17 @@
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetFramework
</artifactId>
<version>
0.2.0-DEV
</version>
<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>
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>
<repositories>
<repository>
...
...
@@ -96,101 +94,4 @@
<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>