Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
What's new
7
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Open sidebar
Mirrors
biopet.biopet
Commits
3150e28e
Commit
3150e28e
authored
Mar 28, 2017
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Upgrade to scala 2.11
parent
3af64e62
Changes
22
Hide whitespace changes
Inline
Side-by-side
Showing
22 changed files
with
34 additions
and
275 deletions
+34
-275
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
+1
-13
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
+3
-21
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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -41,18 +41,6 @@
<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>
...
...
@@ -71,7 +59,7 @@
</dependency>
<dependency>
<groupId>
org.scalatra.scalate
</groupId>
<artifactId>
scalate-core_2.1
0
</artifactId>
<artifactId>
scalate-core_2.1
1
</artifactId>
<version>
1.7.0
</version>
</dependency>
</dependencies>
...
...
biopet-extensions/pom.xml
View file @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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>
...
...
@@ -80,12 +62,12 @@
</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>
<artifactId>
scopt_2.1
1
</artifactId>
<version>
3.3.0
</version>
</dependency>
</dependencies>
...
...
carp/pom.xml
View file @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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
@
f6b20e96
Compare
7805065f
...
f6b20e96
Subproject commit
7805065f00df24c58948ea9961a4
e9
3
93
ae64c70
Subproject commit
f6b20e96f909bd5eb67
e993
ff28a1bdc97b1b23f
gears/pom.xml
View file @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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 @
3150e28e
...
...
@@ -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>
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment