Commit 103babcf authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
Browse files

Merge branch 'develop' into fix-BIOPET-521

parents e37f8612 6abbb191
...@@ -14,7 +14,7 @@ Full documantation is here: [Biopet documantation](http://biopet-docs.readthedoc ...@@ -14,7 +14,7 @@ Full documantation is here: [Biopet documantation](http://biopet-docs.readthedoc
Biopet is available as a JAR package in SHARK. The easiest way to start using it is to activate the `biopet` environment module, which sets useful aliases and environment variables: Biopet is available as a JAR package in SHARK. The easiest way to start using it is to activate the `biopet` environment module, which sets useful aliases and environment variables:
~~~ ~~~
$ module load biopet/v0.6.0 $ module load biopet/v0.8.0
~~~ ~~~
With each Biopet release, an accompanying environment module is also released. The latest release is version 0.4.0, thus `biopet/v0.4.0` is the module you would want to load. With each Biopet release, an accompanying environment module is also released. The latest release is version 0.4.0, thus `biopet/v0.4.0` is the module you would want to load.
......
...@@ -26,7 +26,7 @@ ...@@ -26,7 +26,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
......
...@@ -24,7 +24,7 @@ ...@@ -24,7 +24,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
......
...@@ -31,7 +31,7 @@ ...@@ -31,7 +31,7 @@
<parent> <parent>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
......
/**
* 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 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.basty package nl.lumc.sasc.biopet.pipelines.basty
import java.io.{ File, FileOutputStream } import java.io.{ File, FileOutputStream }
......
...@@ -21,7 +21,7 @@ ...@@ -21,7 +21,7 @@
<parent> <parent>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
<relativePath>../</relativePath> <relativePath>../</relativePath>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
......
/**
* 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 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 package nl.lumc.sasc.biopet.core
import java.io.{ File, PrintWriter } import java.io.{ File, PrintWriter }
......
/**
* 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 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 package nl.lumc.sasc.biopet.core
import java.io.{ File, PrintWriter } import java.io.{ File, PrintWriter }
......
/**
* 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 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 package nl.lumc.sasc.biopet.core
import java.io.{ File, PrintWriter } import java.io.{ File, PrintWriter }
......
/**
* 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 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.annotation package nl.lumc.sasc.biopet.core.annotation
import java.io.File import java.io.File
......
...@@ -21,7 +21,7 @@ ...@@ -21,7 +21,7 @@
<parent> <parent>
<artifactId>Biopet</artifactId> <artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<version>0.8.0-SNAPSHOT</version> <version>0.9.0-SNAPSHOT</version>
</parent> </parent>
<modelVersion>4.0.0</modelVersion> <modelVersion>4.0.0</modelVersion>
......
#
# 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 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.
#
import argparse import argparse
from os.path import join from os.path import join
......
/**
* 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 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.extensions package nl.lumc.sasc.biopet.extensions
import java.io.File import java.io.File
......
/**
* 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 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.extensions package nl.lumc.sasc.biopet.extensions
import java.io.File import java.io.File
......
/**
* 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 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.extensions.centrifuge package nl.lumc.sasc.biopet.extensions.centrifuge
import java.io.File import java.io.File
......
/**
* 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 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.extensions.centrifuge package nl.lumc.sasc.biopet.extensions.centrifuge
import java.io.File import java.io.File
......
/**
* 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 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.extensions.gatk package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File import java.io.File
......
/**
* 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 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.extensions.xhmm package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File import java.io.File
......
/**
* 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 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.extensions.xhmm package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File import java.io.File
......
/**
* 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 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.extensions.xhmm package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File import java.io.File
......
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