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Merge pull request #531 from broadinstitute/ks_build_patches 

Build patches
This commit is contained in:
droazen 2014-02-24 15:13:16 -05:00
parent 1c7eac50fc 7e516b294f
commit e8ea9f58d3
15 changed files with 78 additions and 37 deletions
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35
pom.xml
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@ -715,6 +715,14 @@
<id>unlink-public-testdata</id>
<phase>clean</phase>
</execution>
<execution>
<id>link-public-qscript</id>
<phase>process-test-resources</phase>
</execution>
<execution>
<id>unlink-public-qscript</id>
<phase>clean</phase>
</execution>
</executions>
</plugin>
<plugin>
@ -802,6 +810,33 @@
<modules>
<module>private</module>
</modules>
<build>
<plugins>
<!-- TODO: All tests require access to private. For now. -->
<plugin>
<groupId>com.pyx4j</groupId>
<artifactId>maven-junction-plugin</artifactId>
<executions>
<execution>
<id>link-private-testdata</id>
<phase>process-test-resources</phase>
</execution>
<execution>
<id>unlink-private-testdata</id>
<phase>clean</phase>
</execution>
<execution>
<id>link-private-qscript</id>
<phase>process-test-resources</phase>
</execution>
<execution>
<id>unlink-private-qscript</id>
<phase>clean</phase>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<!-- Collection of properties for use during package testing -->

4
protected/gatk-protected/pom.xml
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@ -31,8 +31,8 @@
</dependency>
<dependency>
<groupId>gov.nist</groupId>
<artifactId>Jama</artifactId>
<groupId>gov.nist.math</groupId>
<artifactId>jama</artifactId>
</dependency>
<dependency>

20
public/external-example/pom.xml
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@ -26,6 +26,9 @@
<sting.committests.skipped>true</sting.committests.skipped>
<sting.unittests.skipped>${sting.committests.skipped}</sting.unittests.skipped>
<sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped>
<!-- This flag is used by the package tests to disable re-shading -->
<sting.shade.phase>package</sting.shade.phase>
</properties>
<repositories>
@ -128,7 +131,7 @@
<version>2.1</version>
<executions>
<execution>
<phase>package</phase>
<phase>${sting.shade.phase}</phase>
<goals>
<goal>shade</goal>
</goals>
@ -246,4 +249,19 @@
</plugins>
</build>
<profiles>
<profile>
<id>packagetests-enabled</id>
<activation>
<property>
<name>sting.packagetests.enabled</name>
<value>true</value>
</property>
</activation>
<properties>
<sting.shade.phase>none</sting.shade.phase>
</properties>
</profile>
</profiles>
</project>

1
public/gatk-package/pom.xml
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@ -57,6 +57,7 @@
<artifactId>gatk-framework</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>

11
public/queue-framework/pom.xml
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@ -61,6 +61,14 @@
<scope>runtime</scope>
</dependency>
<!--
NOTE: Because exec-maven-plugin is used, this aggregator dependency
will cause mvn compile to not work. Use mvn test-compile for now.
See:
http://stackoverflow.com/questions/4786881/why-is-test-jar-dependency-required-for-mvn-compile
http://jira.codehaus.org/browse/MEXEC-91
-->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-framework</artifactId>
@ -78,6 +86,9 @@
<build>
<plugins>
<!--
See note above about exec plugin breaking mvn compile
-->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>

2
public/queue-package/pom.xml
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@ -88,6 +88,7 @@
<artifactId>queue-framework</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
@ -95,6 +96,7 @@
<artifactId>gatk-framework</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>

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public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.jar
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9
public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom
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@ -1,9 +0,0 @@
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.google.code.caliper</groupId>
<artifactId>caliper</artifactId>
<name>caliper</name>
<version>1.0-SNAPSHOT</version>
</project>

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public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.jar
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9
public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom
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@ -1,9 +0,0 @@
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>gov.nist</groupId>
<artifactId>Jama</artifactId>
<name>Jama</name>
<version>1.0.2</version>
</project>

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public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.jar
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9
public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom
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@ -1,9 +0,0 @@
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>net.sf.gridscheduler</groupId>
<artifactId>drmaa</artifactId>
<name>drmaa</name>
<version>6.2u5p2</version>
</project>

11
public/sting-root/pom.xml
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@ -141,8 +141,8 @@
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>gov.nist</groupId>
<artifactId>Jama</artifactId>
<groupId>gov.nist.math</groupId>
<artifactId>jama</artifactId>
<version>1.0.2</version>
</dependency>
<dependency>
@ -201,9 +201,9 @@
<version>0.8.1</version>
</dependency>
<dependency>
<groupId>net.sf.gridscheduler</groupId>
<artifactId>drmaa</artifactId>
<version>6.2u5p2</version>
<groupId>us.levk</groupId>
<artifactId>drmaa-gridengine</artifactId>
<version>6.2u5</version>
</dependency>
<dependency>
<groupId>net.sf.snpeff</groupId>
@ -531,6 +531,7 @@
</extraArguments>
<setReactorProjectsProperties>true</setReactorProjectsProperties>
<descriptionProperty>git.version</descriptionProperty>
<failOutput>exported</failOutput>
</configuration>
<executions>
<execution>

4
public/sting-utils/pom.xml
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@ -93,8 +93,8 @@
<artifactId>jets3t</artifactId>
</dependency>
<dependency>
<groupId>net.sf.gridscheduler</groupId>
<artifactId>drmaa</artifactId>
<groupId>us.levk</groupId>
<artifactId>drmaa-gridengine</artifactId>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>

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settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2-sources.jar
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