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Commit 0906f14b authored by Peter van 't Hof's avatar Peter van 't Hof
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Merge branch 'release-0.6.0' into 'develop' 

Release 0.6.0

This is to merge back changes on the release branch to develop again. First !362  should be done

See merge request !363
parents 43cd6298 b8219d01
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external-example/pom.xml
+ 4
− 4
View file @ 0906f14b
......@@ -11,7 +11,7 @@
<artifactId>ExternalExample</artifactId>
<!--TODO: replace version, for a new pipeline it's advised to start with '0.1.0-SNAPSHOT' -->
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
......@@ -40,19 +40,19 @@
<artifactId>BiopetCore</artifactId>
<!--TODO: replace version of pipeline to a fixed version -->
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetExtensions</artifactId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Shiva</artifactId>
<!--TODO: replace version of pipeline to a fixed version -->
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
</dependency>
</dependencies>
......
pom.xml
+ 1
− 1
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......@@ -9,7 +9,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<relativePath>public</relativePath>
</parent>
......
protected/biopet-gatk-extensions/pom.xml
+ 1
− 1
View file @ 0906f14b
......@@ -15,7 +15,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
protected/biopet-gatk-pipelines/pom.xml
+ 1
− 1
View file @ 0906f14b
......@@ -15,7 +15,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala
+ 5
− 0
View file @ 0906f14b
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
......
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala
+ 5
− 0
View file @ 0906f14b
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
......
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerGvcf.scala
+ 5
− 0
View file @ 0906f14b
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
......
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala
+ 5
− 0
View file @ 0906f14b
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
......
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala
+ 5
− 0
View file @ 0906f14b
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
......
protected/biopet-protected-package/pom.xml
+ 1
− 1
View file @ 0906f14b
......@@ -15,7 +15,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
protected/pom.xml
+ 1
− 1
View file @ 0906f14b
......@@ -11,7 +11,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetRoot</artifactId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<artifactId>BiopetGatk</artifactId>
......
public/bam2wig/pom.xml
+ 1
− 1
View file @ 0906f14b
......@@ -27,7 +27,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
public/bammetrics/pom.xml
+ 1
− 1
View file @ 0906f14b
......@@ -25,7 +25,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/TargetRegions.scala
+ 15
− 0
View file @ 0906f14b
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.pipelines.bammetrics
import java.io.File
......
public/basty/pom.xml
+ 1
− 1
View file @ 0906f14b
......@@ -32,7 +32,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
public/biopet-core/pom.xml
+ 1
− 1
View file @ 0906f14b
......@@ -22,7 +22,7 @@
<parent>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.6.0-SNAPSHOT</version>
<version>0.7.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+ 2
− 2
View file @ 0906f14b
......@@ -83,8 +83,8 @@ trait Reference extends Configurable {
val defaults = ConfigUtils.mergeMaps(this.defaults, this.internalDefaults)
def getReferences(map: Map[String, Any]): Set[(String, String)] = (for (
(species, species_content: Map[String, Any]) <- map.getOrElse("references", Map[String, Any]()).asInstanceOf[Map[String, Any]].toList;
(reference_name, _) <- species_content.toList
(species, species_content) <- map.getOrElse("references", Map[String, Any]()).asInstanceOf[Map[String, Any]].toList;
(reference_name, _) <- species_content.asInstanceOf[Map[String, Any]].toList
) yield (species, reference_name)).toSet
val references = getReferences(defaults) ++ getReferences(Config.global.map)
......
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/annotations/Annotations.scala
+ 15
− 0
View file @ 0906f14b
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.core.annotations
import nl.lumc.sasc.biopet.core.BiopetQScript
......
public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
+ 15
− 0
View file @ 0906f14b
/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project that are
* not part of GATK Queue is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.core
import java.io.File
......
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