Commit 90ca66f2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

version changes

removing source files from jar packaging
parent 683528bf
...@@ -3,13 +3,13 @@ ...@@ -3,13 +3,13 @@
<parent> <parent>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<version>0.1.0</version> <version>0.1.1</version>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet-Framework</artifactId> <artifactId>Biopet-Framework</artifactId>
<name>Biopet-Framework</name> <name>Biopet-Framework</name>
<version>0.1.0</version> <version>0.1.1</version>
<url>http://maven.apache.org</url> <url>http://maven.apache.org</url>
<build> <build>
<plugins> <plugins>
......
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet-Framework</artifactId> <artifactId>Biopet-Framework</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
<packaging>jar</packaging> <packaging>jar</packaging>
<name>Biopet-Framework</name> <name>Biopet-Framework</name>
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
......
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)
}
}
...@@ -3,13 +3,13 @@ ...@@ -3,13 +3,13 @@
<parent> <parent>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<version>0.1.0</version> <version>0.1.1</version>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Flexiprep</artifactId> <artifactId>Flexiprep</artifactId>
<name>Flexiprep</name> <name>Flexiprep</name>
<version>0.1.0</version> <version>0.1.1</version>
<url>http://maven.apache.org</url> <url>http://maven.apache.org</url>
<build> <build>
<resources> <resources>
......
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties> </properties>
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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> <exec.executable>java</exec.executable>
<jpda.listen>true</jpda.listen> <jpda.listen>true</jpda.listen>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
...@@ -41,7 +41,7 @@ ...@@ -41,7 +41,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties> </properties>
......
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Flexiprep</artifactId> <artifactId>Flexiprep</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
<packaging>jar</packaging> <packaging>jar</packaging>
<name>Flexiprep</name> <name>Flexiprep</name>
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
...@@ -45,7 +45,7 @@ ...@@ -45,7 +45,7 @@
<dependency> <dependency>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet-Framework</artifactId> <artifactId>Biopet-Framework</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
</dependency> </dependency>
<!-- <dependency> <!-- <dependency>
<groupId>org.broadinstitute.sting</groupId> <groupId>org.broadinstitute.sting</groupId>
...@@ -55,12 +55,6 @@ ...@@ -55,12 +55,6 @@
</dependencies> </dependencies>
<build> <build>
<resources> <resources>
<resource>
<directory>src/main/java</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
<resource> <resource>
<directory>scripts</directory> <directory>scripts</directory>
<includes> <includes>
......
...@@ -3,13 +3,13 @@ ...@@ -3,13 +3,13 @@
<parent> <parent>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<version>0.1.0</version> <version>0.1.1</version>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Gatk</artifactId> <artifactId>Gatk</artifactId>
<name>Gatk</name> <name>Gatk</name>
<version>0.1.0</version> <version>0.1.1</version>
<url>http://maven.apache.org</url> <url>http://maven.apache.org</url>
<build> <build>
<resources> <resources>
......
{ {
"inputtype": "rna", "inputtype": "rna",
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" }, "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": { "flexiprep": {
"fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"}, "fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"}, "cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
......
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Gatk</artifactId> <artifactId>Gatk</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
<packaging>jar</packaging> <packaging>jar</packaging>
<name>Gatk</name> <name>Gatk</name>
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
...@@ -45,12 +45,12 @@ ...@@ -45,12 +45,12 @@
<dependency> <dependency>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet-Framework</artifactId> <artifactId>Biopet-Framework</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId> <artifactId>Mapping</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.broadinstitute.sting</groupId> <groupId>org.broadinstitute.sting</groupId>
...@@ -60,12 +60,6 @@ ...@@ -60,12 +60,6 @@
</dependencies> </dependencies>
<build> <build>
<resources> <resources>
<resource>
<directory>src/main/java</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
<resource> <resource>
<directory>scripts</directory> <directory>scripts</directory>
<includes> <includes>
......
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"
}
}
...@@ -3,13 +3,13 @@ ...@@ -3,13 +3,13 @@
<parent> <parent>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<version>0.1.0</version> <version>0.1.1</version>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId> <artifactId>Mapping</artifactId>
<name>Mapping</name> <name>Mapping</name>
<version>0.1.0</version> <version>0.1.1</version>
<url>http://maven.apache.org</url> <url>http://maven.apache.org</url>
<build> <build>
<resources> <resources>
......
{ {
"referenceFile": "/blabla/blabla.fa", "referenceFile": "/blabla/blabla.fa",
"fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" }, "fastqc": { "exe": "/home/pjvan_thof/Downloads/FastQC/fastqc" },
"bwa": { "exe": "test" },
"flexiprep": { "flexiprep": {
"fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"}, "fastqc": {"exe":"/home/pjvan_thof/pipelines/test/test"},
"cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"}, "cutadapt": {"exe":"/home/pjvan_thof/pipelines/test/test"},
......
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties> </properties>
...@@ -25,7 +25,7 @@ ...@@ -25,7 +25,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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> <exec.executable>java</exec.executable>
<jpda.listen>true</jpda.listen> <jpda.listen>true</jpda.listen>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
...@@ -41,7 +41,7 @@ ...@@ -41,7 +41,7 @@
<goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal> <goal>org.codehaus.mojo:exec-maven-plugin:1.2.1:exec</goal>
</goals> </goals>
<properties> <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.executable>java</exec.executable>
<exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir> <exec.workingdir>/home/pjvan_thof/pipelines/test</exec.workingdir>
</properties> </properties>
......
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Mapping</artifactId> <artifactId>Mapping</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
<packaging>jar</packaging> <packaging>jar</packaging>
<name>Mapping</name> <name>Mapping</name>
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
...@@ -45,12 +45,12 @@ ...@@ -45,12 +45,12 @@
<dependency> <dependency>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet-Framework</artifactId> <artifactId>Biopet-Framework</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Flexiprep</artifactId> <artifactId>Flexiprep</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.broadinstitute.sting</groupId> <groupId>org.broadinstitute.sting</groupId>
...@@ -60,12 +60,6 @@ ...@@ -60,12 +60,6 @@
</dependencies> </dependencies>
<build> <build>
<resources> <resources>
<resource>
<directory>src/main/java</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
<resource> <resource>
<directory>scripts</directory> <directory>scripts</directory>
<includes> <includes>
......
...@@ -3,7 +3,7 @@ ...@@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.1.0</version> <version>0.1.1</version>
<packaging>pom</packaging> <packaging>pom</packaging>
<name>Biopet</name> <name>Biopet</name>
<modules> <modules>
......
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