version changes

removing source files from jar packaging

biopet-framework/dependency-reduced-pom.xml

@@ -3,13 +3,13 @@
   <parent>
     <artifactId>Biopet</artifactId>
     <groupId>nl.lumc.sasc</groupId>
-    <version>0.1.0</version>
+    <version>0.1.1</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Biopet-Framework</artifactId>
   <name>Biopet-Framework</name>
-  <version>0.1.0</version>
+  <version>0.1.1</version>
   <url>http://maven.apache.org</url>
   <build>
     <plugins>

biopet-framework/pom.xml

@@ -4,7 +4,7 @@
 
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Biopet-Framework</artifactId>
-  <version>0.1.0</version>
+  <version>0.1.1</version>
   <packaging>jar</packaging>
 
   <name>Biopet-Framework</name>
@@ -13,7 +13,7 @@
   <parent>
       <groupId>nl.lumc.sasc</groupId>
       <artifactId>Biopet</artifactId>
-      <version>0.1.0</version>
+      <version>0.1.1</version>
       <relativePath>../</relativePath>
   </parent>
 

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Python.scala

-package nl.lumc.sasc.biopet.function
-
-import java.io.FileOutputStream
-import nl.lumc.sasc.biopet.core._
-import org.broadinstitute.sting.queue.function.CommandLineFunction
-import org.broadinstitute.sting.commandline._
-import java.io.File
-import scala.collection.JavaConversions._
-
-trait Python extends CommandLineFunction {
-  @Argument(doc="Pyhton exe", shortName="script")
-  var python_exe: String = "python"
-  @Input(doc="Pyhton script", shortName="script", required=false)
-  var python_script: File = _
-    
-  private var python_script_name : String = _
-  def setPythonScript(script:String, subpackage:String) {
-    python_script_name = script
-    //val pack = getClass.getPackage.toString.replaceAll(".", "/")
-    //logger.info(pack)
-//    for (r <- getClass.getClassLoader.getResources("/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/*")) {
-//      logger.info(r)
-//      logger.info(r.getContent)
-//    }
-    python_script = new File(".queue/tmp/" + subpackage + python_script_name)
-    if (!python_script.getParentFile.exists) python_script.getParentFile.mkdirs
-    val is = getClass.getResourceAsStream(subpackage + python_script_name)
-    val os = new FileOutputStream(python_script)
-    org.apache.commons.io.IOUtils.copy(is, os)
-    os.close()
-  }
-    
-  def getPythonCommand() : String = {
-    required(python_exe) + required(python_script)
-  }
-}

flexiprep/dependency-reduced-pom.xml

@@ -3,13 +3,13 @@
   <parent>
     <artifactId>Biopet</artifactId>
     <groupId>nl.lumc.sasc</groupId>
-    <version>0.1.0</version>
+    <version>0.1.1</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Flexiprep</artifactId>
   <name>Flexiprep</name>
-  <version>0.1.0</version>
+  <version>0.1.1</version>
   <url>http://maven.apache.org</url>
   <build>
     <resources>

flexiprep/nbactions.xml

@@ -10,7 +10,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>
@@ -25,7 +25,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json</exec.args>
+                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
@@ -41,7 +41,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep -R2 bla.fastq.gz -R1 ../input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/flexiprep/examples/test.json -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>

flexiprep/pom.xml

@@ -4,7 +4,7 @@
 
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Flexiprep</artifactId>
-  <version>0.1.0</version>
+  <version>0.1.1</version>
   <packaging>jar</packaging>
 
   <name>Flexiprep</name>
@@ -13,7 +13,7 @@
   <parent>
       <groupId>nl.lumc.sasc</groupId>
       <artifactId>Biopet</artifactId>
-      <version>0.1.0</version>
+      <version>0.1.1</version>
       <relativePath>../</relativePath>
   </parent>
   
@@ -45,7 +45,7 @@
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Biopet-Framework</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.1</version>
         </dependency>
 <!--        <dependency>
             <groupId>org.broadinstitute.sting</groupId>
@@ -55,12 +55,6 @@
     </dependencies>
     <build>
         <resources>
-            <resource>
-                 <directory>src/main/java</directory>
-                 <includes>
-                     <include>**/*</include>
-                 </includes>
-            </resource>
             <resource>
                  <directory>scripts</directory>
                  <includes>

gatk/dependency-reduced-pom.xml

@@ -3,13 +3,13 @@
   <parent>
     <artifactId>Biopet</artifactId>
     <groupId>nl.lumc.sasc</groupId>
-    <version>0.1.0</version>
+    <version>0.1.1</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Gatk</artifactId>
   <name>Gatk</name>
-  <version>0.1.0</version>
+  <version>0.1.1</version>
   <url>http://maven.apache.org</url>
   <build>
     <resources>

gatk/examples/test.json

 {
     "inputtype": "rna",
     "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
-    "bwa" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
+    "star" : {"exe":"/home/pjvan_thof/pipelines/test/test"},
     "flexiprep": {
         "fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
         "cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},

gatk/pom.xml

@@ -4,7 +4,7 @@
 
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Gatk</artifactId>
-  <version>0.1.0</version>
+  <version>0.1.1</version>
   <packaging>jar</packaging>
 
   <name>Gatk</name>
@@ -13,7 +13,7 @@
   <parent>
       <groupId>nl.lumc.sasc</groupId>
       <artifactId>Biopet</artifactId>
-      <version>0.1.0</version>
+      <version>0.1.1</version>
       <relativePath>../</relativePath>
   </parent>
   
@@ -45,12 +45,12 @@
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Biopet-Framework</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.1</version>
         </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Mapping</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.1</version>
         </dependency>
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
@@ -60,12 +60,6 @@
     </dependencies>
     <build>
         <resources>
-            <resource>
-                 <directory>src/main/java</directory>
-                 <includes>
-                     <include>**/*</include>
-                 </includes>
-            </resource>
             <resource>
                  <directory>scripts</directory>
                  <includes>

gatk/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/modules/BiopetVariantAnnotator.scala

-package nl.lumc.sasc.biopet.pipelines.gatk.modules
-
-import nl.lumc.sasc.biopet.core._
-import org.broadinstitute.sting.queue.QScript
-import org.broadinstitute.sting.queue.extensions.gatk._
-
-class BiopetVariantAnnotator(private var globalConfig: Config) extends QScript with BiopetQScript {
-  qscript =>
-  def this() = this(new Config())
-  
-  @Argument(doc="Config Json file",shortName="config", required=false) var configfiles: List[File] = Nil
-  @Argument(doc="Reference",shortName="R") var referenceFile: File = _
-  @Argument(doc="Variant",shortName="V") var variants: List[File] = Nil
-  @Argument(doc="Output directory", shortName="outputDir", required=false) var outputDir: String = _
-  @Argument(doc="Scattercount",shortName="SC") var scattercount: Int = 0
-  
-  def init {
-    for (file <- configfiles) globalConfig.loadConfigFile(file)
-    config = Config.mergeConfigs(globalConfig.getAsConfig("variantannotator"), globalConfig)
-    if (outputDir == null) outputDir = this.qSettings.runDirectory
-    if (scattercount == 0 && config.contains("scattercount")) scattercount = config.getAsInt("scattercount")
-  }
-  
-  def script {
-    init
-    
-    for (inputFile <- qscript.variants) {
-      val variantAnnotator = new VariantAnnotator with gatkArguments {
-        val config: Config = Config.mergeConfigs(qscript.config.getAsConfig("variantannotator"), qscript.config)
-        this.variant = inputFile
-        if (config.contains("dbsnp")) this.dbsnp = config.getAsString("dbsnp")
-        this.out = swapExt(outputDir, inputFile,".vcf",".annotated.vcf")
-        if (qscript.scattercount > 1) this.scatterCount = qscript.scattercount
-        if (config.contains("scattercount")) this.scatterCount = config.getAsInt("scattercount")
-      }
-      add(variantAnnotator)
-    }
-    
-  }
-  
-  trait gatkArguments extends CommandLineGATK {
-    this.reference_sequence = referenceFile
-    this.memoryLimit = 2
-    this.jobResourceRequests :+= "h_vmem=4G"
-  }
-}

mapping/dependency-reduced-pom.xml

@@ -3,13 +3,13 @@
   <parent>
     <artifactId>Biopet</artifactId>
     <groupId>nl.lumc.sasc</groupId>
-    <version>0.1.0</version>
+    <version>0.1.1</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Mapping</artifactId>
   <name>Mapping</name>
-  <version>0.1.0</version>
+  <version>0.1.1</version>
   <url>http://maven.apache.org</url>
   <build>
     <resources>

mapping/examples/test.json

 {
     "referenceFile": "/blabla/blabla.fa",
     "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
-    
+    "bwa": { "exe": "test" },
     "flexiprep": {
         "fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
         "cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},

mapping/nbactions.xml

@@ -10,7 +10,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN star-2pass -skipflexiprep</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -skipflexiprep -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>
@@ -25,7 +25,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN star-2pass -skipflexiprep</exec.args>
+                <exec.args>-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address} -classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -skipflexiprep -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
@@ -41,7 +41,7 @@
                 <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
             </goals>
             <properties>
-                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN star-2pass -skipflexiprep</exec.args>
+                <exec.args>-classpath %classpath nl.lumc.sasc.biopet.pipelines.mapping.Mapping -R2 bla.fastq.gz -R1 input_R1.fastq -outputDir /home/pjvan_thof/pipelines/test -config /home/pjvan_thof/pipelines/biopet/mapping/examples/test.json -RGLB test -RGSM test -ALN bwa -skipflexiprep -l DEBUG</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
             </properties>

mapping/pom.xml

@@ -4,7 +4,7 @@
 
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Mapping</artifactId>
-  <version>0.1.0</version>
+  <version>0.1.1</version>
   <packaging>jar</packaging>
 
   <name>Mapping</name>
@@ -13,7 +13,7 @@
   <parent>
       <groupId>nl.lumc.sasc</groupId>
       <artifactId>Biopet</artifactId>
-      <version>0.1.0</version>
+      <version>0.1.1</version>
       <relativePath>../</relativePath>
   </parent>
   
@@ -45,12 +45,12 @@
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Biopet-Framework</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.1</version>
         </dependency>
         <dependency>
             <groupId>nl.lumc.sasc</groupId>
             <artifactId>Flexiprep</artifactId>
-            <version>0.1.0</version>
+            <version>0.1.1</version>
         </dependency>
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
@@ -60,12 +60,6 @@
     </dependencies>
     <build>
         <resources>
-            <resource>
-                 <directory>src/main/java</directory>
-                 <includes>
-                     <include>**/*</include>
-                 </includes>
-            </resource>
             <resource>
                  <directory>scripts</directory>
                  <includes>

pom.xml

@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>nl.lumc.sasc</groupId>
   <artifactId>Biopet</artifactId>
-  <version>0.1.0</version>
+  <version>0.1.1</version>
   <packaging>pom</packaging>
   <name>Biopet</name>
   <modules>