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Mirrors
biopet.biopet
Commits
542c87f0
Commit
542c87f0
authored
Mar 29, 2017
by
Peter van 't Hof
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Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-583
parents
5b90369c
23dbd3ee
Changes
23
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23 changed files
with
34 additions
and
286 deletions
+34
-286
bam2wig/pom.xml
bam2wig/pom.xml
+0
-12
bammetrics/pom.xml
bammetrics/pom.xml
+0
-12
basty/pom.xml
basty/pom.xml
+0
-12
biopet-core/pom.xml
biopet-core/pom.xml
+0
-23
biopet-core/src/main/resources/template.ssp
biopet-core/src/main/resources/template.ssp
+0
-0
biopet-extensions/pom.xml
biopet-extensions/pom.xml
+0
-13
biopet-tools-extensions/pom.xml
biopet-tools-extensions/pom.xml
+0
-18
biopet-tools/pom.xml
biopet-tools/pom.xml
+0
-18
biopet-utils/pom.xml
biopet-utils/pom.xml
+4
-22
carp/pom.xml
carp/pom.xml
+0
-12
flexiprep/pom.xml
flexiprep/pom.xml
+0
-12
gatk
gatk
+1
-1
gears/pom.xml
gears/pom.xml
+0
-12
generate-indexes/pom.xml
generate-indexes/pom.xml
+0
-12
gentrap/pom.xml
gentrap/pom.xml
+0
-12
gwas-test/pom.xml
gwas-test/pom.xml
+0
-12
kopisu/pom.xml
kopisu/pom.xml
+0
-12
mapping/pom.xml
mapping/pom.xml
+0
-12
pom.xml
pom.xml
+29
-11
sage/pom.xml
sage/pom.xml
+0
-12
shiva/pom.xml
shiva/pom.xml
+0
-12
tinycap/pom.xml
tinycap/pom.xml
+0
-12
toucan/pom.xml
toucan/pom.xml
+0
-12
No files found.
bam2wig/pom.xml
View file @
542c87f0
...
...
@@ -44,18 +44,6 @@
<artifactId>
BiopetExtensions
</artifactId>
<version>
${project.version}
</version>
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.10
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.testng
</groupId>
<artifactId>
testng
</artifactId>
<version>
6.8
</version>
<scope>
test
</scope>
</dependency>
</dependencies>
</project>
\ No newline at end of file
bammetrics/pom.xml
View file @
542c87f0
...
...
@@ -42,17 +42,5 @@
<artifactId>
BiopetToolsExtensions
</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>
basty/pom.xml
View file @
542c87f0
...
...
@@ -54,17 +54,5 @@
<artifactId>
Mapping
</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>
biopet-core/pom.xml
View file @
542c87f0
...
...
@@ -35,24 +35,6 @@
<artifactId>
BiopetUtils
</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.mockito
</groupId>
<artifactId>
mockito-all
</artifactId>
<version>
1.9.5
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.10
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.broadinstitute.gatk
</groupId>
<artifactId>
gatk-queue
</artifactId>
...
...
@@ -69,11 +51,6 @@
<artifactId>
gatk-queue-extensions-public
</artifactId>
<version>
3.6
</version>
</dependency>
<dependency>
<groupId>
org.scalatra.scalate
</groupId>
<artifactId>
scalate-core_2.10
</artifactId>
<version>
1.7.0
</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file
biopet-core/src/
test
/resources/template.ssp
→
biopet-core/src/
main
/resources/template.ssp
View file @
542c87f0
File moved
biopet-extensions/pom.xml
View file @
542c87f0
...
...
@@ -39,19 +39,6 @@
<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>
<dependency>
<groupId>
org.mockito
</groupId>
<artifactId>
mockito-all
</artifactId>
<version>
1.9.5
</version>
<scope>
test
</scope>
</dependency>
</dependencies>
</project>
\ No newline at end of file
biopet-tools-extensions/pom.xml
View file @
542c87f0
...
...
@@ -43,24 +43,6 @@
<artifactId>
BiopetTools
</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.mockito
</groupId>
<artifactId>
mockito-all
</artifactId>
<version>
1.9.5
</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>
\ No newline at end of file
biopet-tools/pom.xml
View file @
542c87f0
...
...
@@ -29,24 +29,6 @@
<artifactId>
BiopetTools
</artifactId>
<dependencies>
<dependency>
<groupId>
org.testng
</groupId>
<artifactId>
testng
</artifactId>
<version>
6.8
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.mockito
</groupId>
<artifactId>
mockito-all
</artifactId>
<version>
1.9.5
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.10
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetUtils
</artifactId>
...
...
biopet-utils/pom.xml
View file @
542c87f0
...
...
@@ -35,24 +35,6 @@
<artifactId>
colt
</artifactId>
<version>
1.2.0
</version>
</dependency>
<dependency>
<groupId>
org.testng
</groupId>
<artifactId>
testng
</artifactId>
<version>
6.8
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.mockito
</groupId>
<artifactId>
mockito-all
</artifactId>
<version>
1.9.5
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.10
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
log4j
</groupId>
<artifactId>
log4j
</artifactId>
...
...
@@ -71,7 +53,7 @@
<dependency>
<groupId>
org.scala-lang
</groupId>
<artifactId>
scala-library
</artifactId>
<version>
2.1
0
.4
</version>
<version>
2.1
1
.4
</version>
</dependency>
<dependency>
<groupId>
org.yaml
</groupId>
...
...
@@ -80,13 +62,13 @@
</dependency>
<dependency>
<groupId>
io.argonaut
</groupId>
<artifactId>
argonaut_2.1
0
</artifactId>
<artifactId>
argonaut_2.1
1
</artifactId>
<version>
6.1-M4
</version>
</dependency>
<dependency>
<groupId>
com.github.scopt
</groupId>
<artifactId>
scopt_2.1
0
</artifactId>
<version>
3.
3
.0
</version>
<artifactId>
scopt_2.1
1
</artifactId>
<version>
3.
5
.0
</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file
carp/pom.xml
View file @
542c87f0
...
...
@@ -42,17 +42,5 @@
<artifactId>
Mapping
</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>
flexiprep/pom.xml
View file @
542c87f0
...
...
@@ -42,17 +42,5 @@
<artifactId>
BiopetToolsExtensions
</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>
gatk
@
86ee6287
Compare
7805065f
...
86ee6287
Subproject commit
7805065f00df24c58948ea9961a4e9393ae64c70
Subproject commit
86ee6287b66562544e701f9ffa7cbbf0af9f3eba
gears/pom.xml
View file @
542c87f0
...
...
@@ -47,18 +47,6 @@
<artifactId>
BiopetToolsExtensions
</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>
generate-indexes/pom.xml
View file @
542c87f0
...
...
@@ -44,18 +44,6 @@
<artifactId>
BiopetToolsExtensions
</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>
\ No newline at end of file
gentrap/pom.xml
View file @
542c87f0
...
...
@@ -42,17 +42,5 @@
<artifactId>
Mapping
</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>
gwas-test/pom.xml
View file @
542c87f0
...
...
@@ -44,18 +44,6 @@
<artifactId>
BiopetToolsExtensions
</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>
\ No newline at end of file
kopisu/pom.xml
View file @
542c87f0
...
...
@@ -47,17 +47,5 @@
<artifactId>
BiopetToolsExtensions
</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>
mapping/pom.xml
View file @
542c87f0
...
...
@@ -52,18 +52,6 @@
<artifactId>
BamMetrics
</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>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
Bam2Wig
</artifactId>
...
...
pom.xml
View file @
542c87f0
...
...
@@ -53,10 +53,36 @@
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
<scoverage.plugin.version>
1.1.1
</scoverage.plugin.version>
<scalaVersion>
2.1
0
.4
</scalaVersion>
<scalaVersion>
2.1
1
.4
</scalaVersion>
<scoverage.aggregate>
true
</scoverage.aggregate>
</properties>
<dependencies>
<dependency>
<groupId>
org.testng
</groupId>
<artifactId>
testng
</artifactId>
<version>
6.8
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.mockito
</groupId>
<artifactId>
mockito-all
</artifactId>
<version>
1.9.5
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.scalatest
</groupId>
<artifactId>
scalatest_2.11
</artifactId>
<version>
2.2.1
</version>
<scope>
test
</scope>
</dependency>
<dependency>
<groupId>
org.scalatra.scalate
</groupId>
<artifactId>
scalate-core_2.11
</artifactId>
<version>
1.7.0
</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>
${basedir}/src/main/scala
</sourceDirectory>
<testSourceDirectory>
${basedir}/src/test/scala
</testSourceDirectory>
...
...
@@ -129,7 +155,7 @@
</plugin>
<plugin>
<groupId>
org.scalatra.scalate
</groupId>
<artifactId>
maven-scalate-plugin_2.1
0
</artifactId>
<artifactId>
maven-scalate-plugin_2.1
1
</artifactId>
<version>
1.7.0
</version>
<executions>
<execution>
...
...
@@ -296,12 +322,4 @@
</plugin>
</plugins>
</reporting>
<dependencies>
<dependency>
<groupId>
org.scalatra.scalate
</groupId>
<artifactId>
scalate-core_2.10
</artifactId>
<version>
1.7.0
</version>
</dependency>
</dependencies>
</project>
sage/pom.xml
View file @
542c87f0
...
...
@@ -42,17 +42,5 @@
<artifactId>
Mapping
</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>
shiva/pom.xml
View file @
542c87f0
...
...
@@ -49,18 +49,6 @@
<artifactId>
Toucan
</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>
\ No newline at end of file
tinycap/pom.xml
View file @
542c87f0
...
...
@@ -39,18 +39,6 @@
<artifactId>
Gentrap
</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>
\ No newline at end of file
toucan/pom.xml
View file @
542c87f0
...
...
@@ -42,17 +42,5 @@
<artifactId>
BiopetToolsExtensions
</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>
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