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biopet.biopet
Commits
9a265e04
Commit
9a265e04
authored
Nov 22, 2014
by
Peter van 't Hof
Browse files
Added protected packaging
parent
12156894
Changes
4
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protected/biopet-protected-package/.gitignore
0 → 100644
View file @
9a265e04
/target/
\ No newline at end of file
protected/biopet-protected-package/pom.xml
0 → 100644
View file @
9a265e04
<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>
BiopetProtectedPackage
</artifactId>
<version>
0.2.0-DEV
</version>
<packaging>
jar
</packaging>
<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>
<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>
protected/biopet-protected-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutableProtected.scala
0 → 100644
View file @
9a265e04
package
nl.lumc.sasc.biopet.core
object
BiopetExecutableProtected
extends
BiopetExecutable
{
val
pipelines
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
flexiprep
.
Flexiprep
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
mapping
.
Mapping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gentrap
.
Gentrap
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
bammetrics
.
BamMetrics
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkBenchmarkGenotyping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkGenotyping
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVariantcalling
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkPipeline
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVariantRecalibration
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
gatk
.
GatkVcfSampleCompare
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
sage
.
Sage
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
yamsvp
.
Yamsvp
)
val
tools
:
List
[
MainCommand
]
=
List
(
nl
.
lumc
.
sasc
.
biopet
.
tools
.
WipeReads
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
ExtractAlignedFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BiopetFlagstat
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
CheckAllelesVcfInBam
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfToTsv
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfFilter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FindRepeatsPacBio
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedToInterval
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MpileupToVcf
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSplitter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedtoolsCoverageToCounts
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCountFastq
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateLibrary
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateTagCounts
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BastyGenerateFasta
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeAlleles
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SamplesTsvToJson
)
}
protected/pom.xml
View file @
9a265e04
...
...
@@ -12,6 +12,7 @@
<module>
biopet-gatk-extensions
</module>
<module>
biopet-gatk-pipelines
</module>
<module>
basty
</module>
<module>
biopet-protected-package
</module>
</modules>
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
...
...
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