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biopet.biopet
Commit 3150e28e authored by Peter van 't Hof's avatar Peter van 't Hof
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Upgrade to scala 2.11

parent 3af64e62
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Showing with 34 additions and 275 deletions
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>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
biopet-core/pom.xml
View file @ 3150e28e
......@@ -41,18 +41,6 @@
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.9.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue</artifactId>
......@@ -71,7 +59,7 @@
</dependency>
<dependency>
<groupId>org.scalatra.scalate</groupId>
<artifactId>scalate-core_2.10</artifactId>
<artifactId>scalate-core_2.11</artifactId>
<version>1.7.0</version>
</dependency>
</dependencies>
......
biopet-extensions/pom.xml
View file @ 3150e28e
......@@ -39,19 +39,6 @@
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.9.5</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
\ No newline at end of file
biopet-tools-extensions/pom.xml
View file @ 3150e28e
......@@ -43,24 +43,6 @@
<artifactId>BiopetTools</artifactId>
<version>${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>2.10.4</version>
<version>2.11.4</version>
</dependency>
<dependency>
<groupId>org.yaml</groupId>
......@@ -80,12 +62,12 @@
</dependency>
<dependency>
<groupId>io.argonaut</groupId>
<artifactId>argonaut_2.10</artifactId>
<artifactId>argonaut_2.11</artifactId>
<version>6.1-M4</version>
</dependency>
<dependency>
<groupId>com.github.scopt</groupId>
<artifactId>scopt_2.10</artifactId>
<artifactId>scopt_2.11</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
Subproject commit 7805065f00df24c58948ea9961a4e9393ae64c70
Subproject commit f6b20e96f909bd5eb67e993ff28a1bdc97b1b23f
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>2.10.4</scalaVersion>
<scalaVersion>2.11.4</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_2.10</artifactId>
<artifactId>maven-scalate-plugin_2.11</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>
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