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biopet.biopet
Commits
2f47af7e
Commit
2f47af7e
authored
Jul 21, 2014
by
Peter van 't Hof
Browse files
Collected all gatk pipelines/artifacts into 1 maven project
parent
79435a29
Changes
10
Hide whitespace changes
Inline
Side-by-side
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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