Switch to scala 2.10

protected/biopet-gatk-pipelines/pom.xml

@@ -57,7 +57,7 @@
         </dependency>
         <dependency>
             <groupId>org.scalatest</groupId>
-            <artifactId>scalatest_2.11</artifactId>
+            <artifactId>scalatest_2.10</artifactId>
             <version>2.2.1</version>
             <scope>test</scope>
         </dependency>

public/biopet-framework/pom.xml

@@ -55,14 +55,14 @@
         </dependency>
         <dependency>
             <groupId>org.scalatest</groupId>
-            <artifactId>scalatest_2.11</artifactId>
+            <artifactId>scalatest_2.10</artifactId>
             <version>2.2.1</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.scala-lang</groupId>
             <artifactId>scala-library</artifactId>
-            <version>2.11.2</version>
+            <version>2.10.2</version>
         </dependency>
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>
@@ -87,7 +87,7 @@
         </dependency>
         <dependency>
             <groupId>io.argonaut</groupId>
-            <artifactId>argonaut_2.11</artifactId>
+            <artifactId>argonaut_2.10</artifactId>
             <version>6.1-M4</version>
         </dependency>
         <dependency>
@@ -110,5 +110,10 @@
             <artifactId>scopt_2.10</artifactId>
             <version>3.3.0</version>
         </dependency>
+        <dependency>
+            <groupId>org.scalatra.scalate</groupId>
+            <artifactId>scalate-core_2.10</artifactId>
+            <version>1.7.0</version>
+        </dependency>
     </dependencies>
 </project>

public/carp/pom.xml

@@ -52,7 +52,7 @@
         </dependency>
         <dependency>
             <groupId>org.scalatest</groupId>
-            <artifactId>scalatest_2.11</artifactId>
+            <artifactId>scalatest_2.10</artifactId>
             <version>2.2.1</version>
             <scope>test</scope>
         </dependency>

public/flexiprep/pom.xml

@@ -47,7 +47,7 @@
         </dependency>
         <dependency>
             <groupId>org.scalatest</groupId>
-            <artifactId>scalatest_2.11</artifactId>
+            <artifactId>scalatest_2.10</artifactId>
             <version>2.2.1</version>
             <scope>test</scope>
         </dependency>

public/gentrap/pom.xml

@@ -52,7 +52,7 @@
         </dependency>
         <dependency>
             <groupId>org.scalatest</groupId>
-            <artifactId>scalatest_2.11</artifactId>
+            <artifactId>scalatest_2.10</artifactId>
             <version>2.2.1</version>
             <scope>test</scope>
         </dependency>

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/CufflinksProducer.scala

@@ -21,12 +21,17 @@ import scalaz._, Scalaz._
 import nl.lumc.sasc.biopet.extensions.{ Cufflinks, Ln }
 
 /** General trait for containing cufflinks results */
-trait CufflinksProducer { this: Gentrap#Sample =>
+trait CufflinksProducer {
 
   import Gentrap._
   import Gentrap.ExpMeasures._
   import Gentrap.StrandProtocol._
 
+  protected def sampleDir: File
+  protected def sampleId: String
+  protected def pipeline: Gentrap
+  protected def alnFile: File
+
   /** Valid cufflink measure types */
   protected val cufflinksMeasures = Set(CufflinksStrict, CufflinksGuided, CufflinksBlind)
 

public/mapping/pom.xml

@@ -57,7 +57,7 @@
         </dependency>
         <dependency>
             <groupId>org.scalatest</groupId>
-            <artifactId>scalatest_2.11</artifactId>
+            <artifactId>scalatest_2.10</artifactId>
             <version>2.2.1</version>
             <scope>test</scope>
 	    </dependency>

public/pom.xml

@@ -210,7 +210,7 @@
               <artifactId>scoverage-maven-plugin</artifactId>
               <version>${scoverage.plugin.version}</version>
               <configuration>
-                  <scalaVersion>2.11.4</scalaVersion>
+                  <scalaVersion>2.10.2</scalaVersion>
                   <!-- other parameters -->
               </configuration>
             </plugin>

public/shiva/pom.xml

@@ -48,7 +48,7 @@
         </dependency>
         <dependency>
             <groupId>org.scalatest</groupId>
-            <artifactId>scalatest_2.11</artifactId>
+            <artifactId>scalatest_2.10</artifactId>
             <version>2.2.1</version>
             <scope>test</scope>
         </dependency>