Commit d61516a5 authored by Peter van 't Hof's avatar Peter van 't Hof

Remove protected dir

parent b10509f2
......@@ -37,9 +37,6 @@
<module>../public/biopet-tools-extensions</module>
<module>../public/biopet-extensions</module>
<module>../public/biopet-tools-package</module>
<module>../protected/biopet-gatk-extensions</module>
<module>../protected/biopet-gatk-pipelines</module>
<module>../protected/biopet-protected-package</module>
</modules>
</project>
\ No newline at end of file
......@@ -15,8 +15,6 @@
<modules>
<module>public</module>
<module>protected</module>
<module>external-example</module>
<!--<module>biopet-aggregate</module>-->
</modules>
</project>
biopet-gatk-extensions/src/main/resources/nl/lumc/sasc/biopet/License.txt
\ No newline at end of file
/target/
\ No newline at end of file
<!--
Due to the license issue with GATK, this part of Biopet can only be used inside the
LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
on how to use this protected part of biopet or contact us at sasc@lumc.nl
-->
<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>
<artifactId>BiopetGatkExtensions</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>BiopetGatkExtensions</name>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<!--<dependency>-->
<!--<groupId>org.broadinstitute.gatk</groupId>-->
<!--<artifactId>gatk-queue-extensions-distribution</artifactId>-->
<!--<version>3.5</version>-->
<!--<exclusions>-->
<!--&lt;!&ndash; This exclusion is needed for the selective licence for Queue &ndash;&gt;-->
<!--<exclusion>-->
<!--<groupId>org.broadinstitute.gatk</groupId>-->
<!--<artifactId>gatk-tools-protected</artifactId>-->
<!--</exclusion>-->
<!--</exclusions>-->
<!--</dependency>-->
</dependencies>
</project>
Due to the license issue with GATK, this part of Biopet can only be used inside the
LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=ERROR, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
/target/
\ No newline at end of file
<!--
Due to the license issue with GATK, this part of Biopet can only be used inside the
LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
on how to use this protected part of biopet or contact us at sasc@lumc.nl
-->
<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>
<artifactId>BiopetGatkPipelines</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>BiopetGatkPipelines</name>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatkExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Basty</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Shiva</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
#
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=ERROR, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
@HD VN:1.4 SO:unsorted
@SQ SN:chr1 LN:9 UR:file:/home/pjvan_thof/pipelines/biopet/public/mapping/src/test/resources/ref.fa M5:fe15dbbd0900310caf32827f6da57550
<!--
Due to the license issue with GATK, this part of Biopet can only be used inside the
LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
on how to use this protected part of biopet or contact us at sasc@lumc.nl
-->
<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>
<artifactId>BiopetProtectedPackage</artifactId>
<packaging>jar</packaging>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<inceptionYear>2014</inceptionYear>
<name>BiopetProtectedPackage</name>
<properties>
<sting.shade.phase>package</sting.shade.phase>
<app.main.class>nl.lumc.sasc.biopet.BiopetExecutableProtected</app.main.class>
</properties>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetPublicPackage</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatkPipelines</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Basty</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.1</version>
<configuration>
<!--suppress MavenModelInspection -->
<finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>${app.main.class}</Main-Class>
<!--suppress MavenModelInspection -->
<X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
<!--suppress MavenModelInspection -->
<X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
</manifestEntries>
</transformer>
</transformers>
<filters>
<filter>
<artifact>nl.lumc.sasc:BiopetFramework</artifact>
<excludes>
<exclude>nl/lumc/sasc/biopet/License.txt</exclude>
</excludes>
</filter>
</filters>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
#
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=ERROR, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
#
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=ERROR, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<!--
Due to the license issue with GATK, this part of Biopet can only be used inside the
LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
on how to use this protected part of biopet or contact us at sasc@lumc.nl
-->
<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>
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetRoot</artifactId>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<artifactId>BiopetGatk</artifactId>
<name>BiopetGatk</name>
<packaging>pom</packaging>
<modules>
<module>biopet-gatk-extensions</module>
<module>biopet-gatk-pipelines</module>
<module>biopet-protected-package</module>
</modules>
</project>
\ No newline at end of file
#
# Due to the license issue with GATK, this part of Biopet can only be used inside the
# LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
# on how to use this protected part of biopet or contact us at sasc@lumc.nl
#
# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=ERROR, A1
# A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender
# A1 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%-5p [%d] [%C{1}] - %m%n
\ No newline at end of file
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