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biopet.biopet
Commits
7dd149bd
Commit
7dd149bd
authored
Mar 29, 2017
by
Peter van 't Hof
Browse files
Merge remote-tracking branch 'remotes/origin/develop' into epic-summary_reformat
parents
f9f9a24c
23dbd3ee
Changes
23
Hide whitespace changes
Inline
Side-by-side
bam2wig/pom.xml
View file @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
File moved
biopet-extensions/pom.xml
View file @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -50,24 +50,6 @@
<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>
...
...
@@ -86,7 +68,7 @@
<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>
...
...
@@ -95,13 +77,13 @@
</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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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 @
7dd149bd
...
...
@@ -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>
...
...
@@ -130,7 +156,7 @@
</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>
...
...
@@ -297,12 +323,4 @@
</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 @
7dd149bd
...
...
@@ -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>
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