From 26ea8a5026590c7d663fc6ed0590d68b0f3a729f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 29 Jan 2015 16:23:03 +0100
Subject: [PATCH] Init framework for BamToBigWig
---
.../BiopetProtectedPackage.iml | 1 +
public/bamtobigwig/bamtobigwig.iml | 94 +++++++++++++++++++
public/bamtobigwig/pom.xml | 29 ++++++
.../pipelines/bamtobigwig/BamToBigWig.scala | 20 ++++
public/biopet-framework/BiopetFramework.iml | 5 +
.../BiopetPublicPackage.iml | 1 +
public/biopet-public-package/pom.xml | 5 +
.../biopet/core/BiopetExecutablePublic.scala | 3 +-
public/pom.xml | 1 +
9 files changed, 158 insertions(+), 1 deletion(-)
create mode 100644 public/bamtobigwig/bamtobigwig.iml
create mode 100644 public/bamtobigwig/pom.xml
create mode 100644 public/bamtobigwig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToBigWig.scala
diff --git a/protected/biopet-protected-package/BiopetProtectedPackage.iml b/protected/biopet-protected-package/BiopetProtectedPackage.iml
index 65380feeb..dacf9db7b 100644
--- a/protected/biopet-protected-package/BiopetProtectedPackage.iml
+++ b/protected/biopet-protected-package/BiopetProtectedPackage.iml
@@ -95,6 +95,7 @@
<orderEntry type="module" module-name="Gentrap" />
<orderEntry type="module" module-name="Sage" />
<orderEntry type="module" module-name="Yamsvp" />
+ <orderEntry type="module" module-name="bamtobigwig" />
<orderEntry type="module" module-name="BiopetGatkPipelines" />
<orderEntry type="module" module-name="BiopetGatkExtensions" />
<orderEntry type="module" module-name="Basty" />
diff --git a/public/bamtobigwig/bamtobigwig.iml b/public/bamtobigwig/bamtobigwig.iml
new file mode 100644
index 000000000..7c23856fd
--- /dev/null
+++ b/public/bamtobigwig/bamtobigwig.iml
@@ -0,0 +1,94 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+ <component name="NewModuleRootManager" inherit-compiler-output="false">
+ <output url="file://$MODULE_DIR$/target/classes" />
+ <output-test url="file://$MODULE_DIR$/target/test-classes" />
+ <content url="file://$MODULE_DIR$">
+ <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
+ <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
+ <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
+ <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
+ <excludeFolder url="file://$MODULE_DIR$/target" />
+ </content>
+ <orderEntry type="inheritedJdk" />
+ <orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="module" module-name="BiopetFramework" />
+ <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
+ <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
+ <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
+ <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
+ <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
+ <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
+ <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
+ <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
+ <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
+ <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
+ <orderEntry type="module-library">
+ <library name="Maven: com.sun:tools:1.4.2">
+ <CLASSES>
+ <root url="jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/" />
+ </CLASSES>
+ <JAVADOC />
+ <SOURCES />
+ </library>
+ </orderEntry>
+ <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
+ <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
+ <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
+ <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
+ <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
+ <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
+ <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
+ <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
+ <orderEntry type="module-library">
+ <library name="Maven: com.sun:tools.jar:1.5">
+ <CLASSES>
+ <root url="jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/" />
+ </CLASSES>
+ <JAVADOC />
+ <SOURCES />
+ </library>
+ </orderEntry>
+ <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
+ <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
+ <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
+ <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
+ <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
+ <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
+ <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
+ <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
+ <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+ <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
+ <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
+ <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
+ <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
+ <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
+ <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
+ <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
+ <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
+ <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
+ <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
+ <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
+ <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
+ <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
+ <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
+ <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
+ <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
+ <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
+ <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
+ <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
+ <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
+ <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
+ <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
+ <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
+ <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
+ <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
+ <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
+ </component>
+</module>
\ No newline at end of file
diff --git a/public/bamtobigwig/pom.xml b/public/bamtobigwig/pom.xml
new file mode 100644
index 000000000..ff29da93b
--- /dev/null
+++ b/public/bamtobigwig/pom.xml
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BamToBigWig</artifactId>
+ <packaging>jar</packaging>
+
+ <parent>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>Biopet</artifactId>
+ <version>0.3.0-DEV</version>
+ <relativePath>../</relativePath>
+ </parent>
+
+ <inceptionYear>2014</inceptionYear>
+ <name>BamToBigWig</name>
+
+ <dependencies>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BiopetFramework</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
\ No newline at end of file
diff --git a/public/bamtobigwig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToBigWig.scala b/public/bamtobigwig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToBigWig.scala
new file mode 100644
index 000000000..1028f6487
--- /dev/null
+++ b/public/bamtobigwig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToBigWig.scala
@@ -0,0 +1,20 @@
+package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import org.broadinstitute.gatk.queue.QScript
+
+/**
+ * Created by pjvan_thof on 1/29/15.
+ */
+class BamToBigWig(val root: Configurable) extends QScript with BiopetQScript {
+ def this() = this(null)
+
+ def init(): Unit = {
+ }
+
+ def biopetScript(): Unit = {
+ }
+}
+
+object BamToBigWig extends PipelineCommand
\ No newline at end of file
diff --git a/public/biopet-framework/BiopetFramework.iml b/public/biopet-framework/BiopetFramework.iml
index d59d5cc47..2650bfa75 100644
--- a/public/biopet-framework/BiopetFramework.iml
+++ b/public/biopet-framework/BiopetFramework.iml
@@ -1,5 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+ <component name="FacetManager">
+ <facet type="Python" name="Python">
+ <configuration sdkName="" />
+ </facet>
+ </component>
<component name="NewModuleRootManager" inherit-compiler-output="false">
<output url="file://$MODULE_DIR$/target/classes" />
<output-test url="file://$MODULE_DIR$/target/test-classes" />
diff --git a/public/biopet-public-package/BiopetPublicPackage.iml b/public/biopet-public-package/BiopetPublicPackage.iml
index 345cfb016..6f4e49931 100644
--- a/public/biopet-public-package/BiopetPublicPackage.iml
+++ b/public/biopet-public-package/BiopetPublicPackage.iml
@@ -94,5 +94,6 @@
<orderEntry type="module" module-name="Gentrap" />
<orderEntry type="module" module-name="Sage" />
<orderEntry type="module" module-name="Yamsvp" />
+ <orderEntry type="module" module-name="bamtobigwig" />
</component>
</module>
\ No newline at end of file
diff --git a/public/biopet-public-package/pom.xml b/public/biopet-public-package/pom.xml
index 696f8f3ae..54bfeddac 100644
--- a/public/biopet-public-package/pom.xml
+++ b/public/biopet-public-package/pom.xml
@@ -75,6 +75,11 @@
<artifactId>Yamsvp</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>nl.lumc.sasc</groupId>
+ <artifactId>BamToBigWig</artifactId>
+ <version>${project.version}</version>
+ </dependency>
</dependencies>
<build>
<plugins>
diff --git a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
index d50a72d5a..00f52a306 100644
--- a/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
+++ b/public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala
@@ -22,7 +22,8 @@ object BiopetExecutablePublic extends BiopetExecutable {
nl.lumc.sasc.biopet.pipelines.gentrap.Gentrap,
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics,
nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp,
- nl.lumc.sasc.biopet.pipelines.sage.Sage
+ nl.lumc.sasc.biopet.pipelines.sage.Sage,
+ nl.lumc.sasc.biopet.pipelines.bamtobigwig.BamToBigWig
)
def tools: List[MainCommand] = List(
diff --git a/public/pom.xml b/public/pom.xml
index a2b8b014c..3097a7bbe 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -33,6 +33,7 @@
<module>mapping</module>
<module>sage</module>
<module>yamsvp</module>
+ <module>bamtobigwig</module>
</modules>
<properties>
--
GitLab