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biopet.biopet
Commits
d61516a5
Commit
d61516a5
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Remove protected dir
parent
b10509f2
Changes
19
Hide whitespace changes
Inline
Side-by-side
biopet-aggregate/pom.xml
View file @
d61516a5
...
...
@@ -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
pom.xml
View file @
d61516a5
...
...
@@ -15,8 +15,6 @@
<modules>
<module>
public
</module>
<module>
protected
</module>
<module>
external-example
</module>
<!--<module>biopet-aggregate</module>-->
</modules>
</project>
protected/LICENSE
deleted
120000 → 0
View file @
b10509f2
biopet-gatk-extensions/src/main/resources/nl/lumc/sasc/biopet/License.txt
\ No newline at end of file
protected/biopet-gatk-extensions/.gitignore
deleted
100644 → 0
View file @
b10509f2
/target/
\ No newline at end of file
protected/biopet-gatk-extensions/pom.xml
deleted
100644 → 0
View file @
b10509f2
<!--
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>-->
<!--<!– This exclusion is needed for the selective licence for Queue –>-->
<!--<exclusion>-->
<!--<groupId>org.broadinstitute.gatk</groupId>-->
<!--<artifactId>gatk-tools-protected</artifactId>-->
<!--</exclusion>-->
<!--</exclusions>-->
<!--</dependency>-->
</dependencies>
</project>
protected/biopet-gatk-extensions/src/main/resources/nl/lumc/sasc/biopet/License.txt
deleted
100644 → 0
View file @
b10509f2
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
protected/biopet-gatk-extensions/src/test/resources/log4j.properties
deleted
100644 → 0
View file @
b10509f2
#
# 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
protected/biopet-gatk-pipelines/.gitignore
deleted
100644 → 0
View file @
b10509f2
/target/
\ No newline at end of file
protected/biopet-gatk-pipelines/pom.xml
deleted
100644 → 0
View file @
b10509f2
<!--
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>
protected/biopet-gatk-pipelines/src/test/resources/log4j.properties
deleted
100644 → 0
View file @
b10509f2
#
# 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
protected/biopet-gatk-pipelines/src/test/resources/ref.dict
deleted
100644 → 0
View file @
b10509f2
@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
protected/biopet-gatk-pipelines/src/test/resources/ref.fa
deleted
100644 → 0
View file @
b10509f2
>chr1
AGTAGTAGT
protected/biopet-gatk-pipelines/src/test/resources/ref.fa.fai
deleted
100644 → 0
View file @
b10509f2
chr1 9 6 9 10
protected/biopet-protected-package/.gitignore
deleted
100644 → 0
View file @
b10509f2
/target/
\ No newline at end of file
protected/biopet-protected-package/pom.xml
deleted
100644 → 0
View file @
b10509f2
<!--
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>
protected/biopet-protected-package/src/test/resources/log4j.properties
deleted
100644 → 0
View file @
b10509f2
#
# 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
protected/log4j.properties
deleted
100644 → 0
View file @
b10509f2
#
# 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
protected/pom.xml
deleted
100644 → 0
View file @
b10509f2
<?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
protected/src/src/test/resources/log4j.properties
deleted
100644 → 0
View file @
b10509f2
#
# 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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