Commit 23dbd3ee authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
Browse files

Merge pull request #46 from biopet/fix-BIOPET-594

Upgrade to scala 2.11
parents 3019cf79 d2a31aa7
...@@ -44,18 +44,6 @@ ...@@ -44,18 +44,6 @@
<artifactId>BiopetExtensions</artifactId> <artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
\ No newline at end of file
...@@ -42,17 +42,5 @@ ...@@ -42,17 +42,5 @@
<artifactId>BiopetToolsExtensions</artifactId> <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
...@@ -54,17 +54,5 @@ ...@@ -54,17 +54,5 @@
<artifactId>Mapping</artifactId> <artifactId>Mapping</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
...@@ -35,24 +35,6 @@ ...@@ -35,24 +35,6 @@
<artifactId>BiopetUtils</artifactId> <artifactId>BiopetUtils</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> <dependency>
<groupId>org.broadinstitute.gatk</groupId> <groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue</artifactId> <artifactId>gatk-queue</artifactId>
...@@ -69,11 +51,6 @@ ...@@ -69,11 +51,6 @@
<artifactId>gatk-queue-extensions-public</artifactId> <artifactId>gatk-queue-extensions-public</artifactId>
<version>3.6</version> <version>3.6</version>
</dependency> </dependency>
<dependency>
<groupId>org.scalatra.scalate</groupId>
<artifactId>scalate-core_2.10</artifactId>
<version>1.7.0</version>
</dependency>
</dependencies> </dependencies>
</project> </project>
\ No newline at end of file
...@@ -39,19 +39,6 @@ ...@@ -39,19 +39,6 @@
<version>6.8</version> <version>6.8</version>
<scope>test</scope> <scope>test</scope>
</dependency> </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> </dependencies>
</project> </project>
\ No newline at end of file
...@@ -43,24 +43,6 @@ ...@@ -43,24 +43,6 @@
<artifactId>BiopetTools</artifactId> <artifactId>BiopetTools</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
\ No newline at end of file
...@@ -29,24 +29,6 @@ ...@@ -29,24 +29,6 @@
<artifactId>BiopetTools</artifactId> <artifactId>BiopetTools</artifactId>
<dependencies> <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> <dependency>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetUtils</artifactId> <artifactId>BiopetUtils</artifactId>
......
...@@ -35,24 +35,6 @@ ...@@ -35,24 +35,6 @@
<artifactId>colt</artifactId> <artifactId>colt</artifactId>
<version>1.2.0</version> <version>1.2.0</version>
</dependency> </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> <dependency>
<groupId>log4j</groupId> <groupId>log4j</groupId>
<artifactId>log4j</artifactId> <artifactId>log4j</artifactId>
...@@ -71,7 +53,7 @@ ...@@ -71,7 +53,7 @@
<dependency> <dependency>
<groupId>org.scala-lang</groupId> <groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId> <artifactId>scala-library</artifactId>
<version>2.10.4</version> <version>2.11.4</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.yaml</groupId> <groupId>org.yaml</groupId>
...@@ -80,13 +62,13 @@ ...@@ -80,13 +62,13 @@
</dependency> </dependency>
<dependency> <dependency>
<groupId>io.argonaut</groupId> <groupId>io.argonaut</groupId>
<artifactId>argonaut_2.10</artifactId> <artifactId>argonaut_2.11</artifactId>
<version>6.1-M4</version> <version>6.1-M4</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.github.scopt</groupId> <groupId>com.github.scopt</groupId>
<artifactId>scopt_2.10</artifactId> <artifactId>scopt_2.11</artifactId>
<version>3.3.0</version> <version>3.5.0</version>
</dependency> </dependency>
</dependencies> </dependencies>
</project> </project>
\ No newline at end of file
...@@ -42,17 +42,5 @@ ...@@ -42,17 +42,5 @@
<artifactId>Mapping</artifactId> <artifactId>Mapping</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
...@@ -42,17 +42,5 @@ ...@@ -42,17 +42,5 @@
<artifactId>BiopetToolsExtensions</artifactId> <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
Subproject commit 7805065f00df24c58948ea9961a4e9393ae64c70 Subproject commit 86ee6287b66562544e701f9ffa7cbbf0af9f3eba
...@@ -47,18 +47,6 @@ ...@@ -47,18 +47,6 @@
<artifactId>BiopetToolsExtensions</artifactId> <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
...@@ -44,18 +44,6 @@ ...@@ -44,18 +44,6 @@
<artifactId>BiopetToolsExtensions</artifactId> <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
\ No newline at end of file
...@@ -42,17 +42,5 @@ ...@@ -42,17 +42,5 @@
<artifactId>Mapping</artifactId> <artifactId>Mapping</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
...@@ -44,18 +44,6 @@ ...@@ -44,18 +44,6 @@
<artifactId>BiopetToolsExtensions</artifactId> <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
\ No newline at end of file
...@@ -47,17 +47,5 @@ ...@@ -47,17 +47,5 @@
<artifactId>BiopetToolsExtensions</artifactId> <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
...@@ -52,18 +52,6 @@ ...@@ -52,18 +52,6 @@
<artifactId>BamMetrics</artifactId> <artifactId>BamMetrics</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> <dependency>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Bam2Wig</artifactId> <artifactId>Bam2Wig</artifactId>
......
...@@ -53,10 +53,36 @@ ...@@ -53,10 +53,36 @@
<properties> <properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<scoverage.plugin.version>1.1.1</scoverage.plugin.version> <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
<scalaVersion>2.10.4</scalaVersion> <scalaVersion>2.11.4</scalaVersion>
<scoverage.aggregate>true</scoverage.aggregate> <scoverage.aggregate>true</scoverage.aggregate>
</properties> </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> <build>
<sourceDirectory>${basedir}/src/main/scala</sourceDirectory> <sourceDirectory>${basedir}/src/main/scala</sourceDirectory>
<testSourceDirectory>${basedir}/src/test/scala</testSourceDirectory> <testSourceDirectory>${basedir}/src/test/scala</testSourceDirectory>
...@@ -129,7 +155,7 @@ ...@@ -129,7 +155,7 @@
</plugin> </plugin>
<plugin> <plugin>
<groupId>org.scalatra.scalate</groupId> <groupId>org.scalatra.scalate</groupId>
<artifactId>maven-scalate-plugin_2.10</artifactId> <artifactId>maven-scalate-plugin_2.11</artifactId>
<version>1.7.0</version> <version>1.7.0</version>
<executions> <executions>
<execution> <execution>
...@@ -296,12 +322,4 @@ ...@@ -296,12 +322,4 @@
</plugin> </plugin>
</plugins> </plugins>
</reporting> </reporting>
<dependencies>
<dependency>
<groupId>org.scalatra.scalate</groupId>
<artifactId>scalate-core_2.10</artifactId>
<version>1.7.0</version>
</dependency>
</dependencies>
</project> </project>
...@@ -42,17 +42,5 @@ ...@@ -42,17 +42,5 @@
<artifactId>Mapping</artifactId> <artifactId>Mapping</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
...@@ -49,18 +49,6 @@ ...@@ -49,18 +49,6 @@
<artifactId>Toucan</artifactId> <artifactId>Toucan</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
\ No newline at end of file
...@@ -39,18 +39,6 @@ ...@@ -39,18 +39,6 @@
<artifactId>Gentrap</artifactId> <artifactId>Gentrap</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
\ No newline at end of file
...@@ -42,17 +42,5 @@ ...@@ -42,17 +42,5 @@
<artifactId>BiopetToolsExtensions</artifactId> <artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </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> </dependencies>
</project> </project>
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