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Commit 2f47af7e authored by Peter van 't Hof's avatar Peter van 't Hof
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Collected all gatk pipelines/artifacts into 1 maven project

parent 79435a29
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bam-metrics/pom.xml
View file @ 2f47af7e
......@@ -54,8 +54,8 @@
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -117,7 +117,7 @@
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:queue-package</exclude>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
......
biopet-framework/pom.xml
View file @ 2f47af7e
......@@ -51,8 +51,8 @@
</dependency>-->
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -121,7 +121,7 @@
</includes>
</filter>
<filter>
<artifact>org.broadinstitute.gatk:queue-package</artifact>
<artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
<excludes>
<!-- <exclude>scala/**</exclude>-->
</excludes>
......
flexiprep/pom.xml
View file @ 2f47af7e
......@@ -49,8 +49,8 @@
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -112,7 +112,7 @@
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:queue-package</exclude>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
......
gatk/gatk-benchmark-genotyping/pom.xml
View file @ 2f47af7e
......@@ -54,8 +54,8 @@
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -117,7 +117,7 @@
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:queue-package</exclude>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
......
gatk/gatk-genotyping/pom.xml
View file @ 2f47af7e
......@@ -49,8 +49,8 @@
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -112,7 +112,7 @@
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:queue-package</exclude>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
......
gatk/gatk-old/pom.xml
View file @ 2f47af7e
......@@ -59,8 +59,8 @@
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -122,7 +122,7 @@
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:queue-package</exclude>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
......
gatk/gatk-pipeline/pom.xml
View file @ 2f47af7e
......@@ -69,8 +69,8 @@
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -132,7 +132,7 @@
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:queue-package</exclude>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
......
gatk/gatk-variantcalling/pom.xml
View file @ 2f47af7e
......@@ -49,8 +49,8 @@
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -112,7 +112,7 @@
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:queue-package</exclude>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
......
mapping/pom.xml
View file @ 2f47af7e
......@@ -59,8 +59,8 @@
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -122,7 +122,7 @@
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:queue-package</exclude>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
......
pipeline-template/pom.xml
View file @ 2f47af7e
......@@ -49,8 +49,8 @@
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>queue-package</artifactId>
<version>3.2-2</version>
<artifactId>gatk-queue-package-distribution</artifactId>
<version>3.2</version>
</dependency>
</dependencies>
<build>
......@@ -112,7 +112,7 @@
</transformers>
<artifactSet>
<excludes>
<exclude>org.broadinstitute.gatk:queue-package</exclude>
<exclude>org.broadinstitute.gatk:gatk-queue-package-distribution</exclude>
<exclude>junit:junit</exclude>
<exclude>org.scala-lang:scala-compiler</exclude>
<exclude>org.scala-lang:scala-library</exclude>
......
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