Skip to content

GitLab

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
Hide whitespace changes
Inline Side-by-side
biopet-framework/dependency-reduced-pom.xml
View file @ 90ca66f2
......@@ -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
View file @ 90ca66f2
......@@ -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 deleted 100644 → 0
View file @ 683528bf
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
View file @ 90ca66f2
......@@ -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
View file @ 90ca66f2
......@@ -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
View file @ 90ca66f2
......@@ -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
View file @ 90ca66f2
......@@ -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
View file @ 90ca66f2
{
"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
View file @ 90ca66f2
......@@ -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 deleted 100644 → 0
View file @ 683528bf
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
View file @ 90ca66f2
......@@ -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
View file @ 90ca66f2
{
"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
View file @ 90ca66f2
......@@ -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
View file @ 90ca66f2
......@@ -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
View file @ 90ca66f2
......@@ -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>
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment