Commit abb2a281 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'release-0.5.0' into develop

parents bd7ca140 ac785920
......@@ -5,7 +5,7 @@
<parent>
<artifactId>BiopetRoot</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
......@@ -33,7 +33,7 @@
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetProtectedPackage</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
......
......@@ -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>0.1.0-SNAPSHOT</version>
<version>0.6.0-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>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetExtensions</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Shiva</artifactId>
<!--TODO: replace version of pipeline to a fixed version -->
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
</dependency>
</dependencies>
......
......@@ -9,7 +9,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
<relativePath>public</relativePath>
</parent>
......
......@@ -15,7 +15,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
......@@ -15,7 +15,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
......@@ -15,7 +15,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetGatk</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
......@@ -11,7 +11,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetRoot</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<artifactId>BiopetGatk</artifactId>
......
biopet-framework/src/main/resources/nl/lumc/sasc/biopet/License.txt
\ No newline at end of file
biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt
\ No newline at end of file
......@@ -27,7 +27,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
......@@ -25,7 +25,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
......@@ -32,7 +32,7 @@
<parent>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Biopet</artifactId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
......
<?xml version="1.0" encoding="UTF-8"?>
<!--
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.
-->
<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">
<parent>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.5.0-SNAPSHOT</version>
<version>0.6.0-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
<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 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.
*/
/*
* Base structure
*/
......
/**
* 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.
*/
/* line 2, ../sass/_sortable.sass */
table[data-sortable] {
border-collapse: collapse;
......
/*
* 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.
*/
/*! sortable.js 0.5.0 */
(function(){var a,b,c,d,e,f;a="table[data-sortable]",c=/^-?[£$¤]?[\d,.]+%?$/,f=/^\s+|\s+$/g,e="ontouchstart"in document.documentElement,b=e?"touchstart":"click",d={init:function(){var b,c,e,f,g;for(c=document.querySelectorAll(a),g=[],e=0,f=c.length;f>e;e++)b=c[e],g.push(d.initTable(b));return g},initTable:function(a){var b,c,e,f,g;if(1===a.tHead.rows.length&&"true"!==a.getAttribute("data-sortable-initialized")){for(a.setAttribute("data-sortable-initialized","true"),e=a.querySelectorAll("th"),b=f=0,g=e.length;g>f;b=++f)c=e[b],"false"!==c.getAttribute("data-sortable")&&d.setupClickableTH(a,c,b);return a}},setupClickableTH:function(a,c,e){var f;return f=d.getColumnType(a,e),c.addEventListener(b,function(){var b,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u;for(j="true"===this.getAttribute("data-sorted"),k=this.getAttribute("data-sorted-direction"),b=j?"ascending"===k?"descending":"ascending":f.defaultSortDirection,m=this.parentNode.querySelectorAll("th"),n=0,q=m.length;q>n;n++)c=m[n],c.setAttribute("data-sorted","false"),c.removeAttribute("data-sorted-direction");for(this.setAttribute("data-sorted","true"),this.setAttribute("data-sorted-direction",b),l=a.tBodies[0],h=[],t=l.rows,o=0,r=t.length;r>o;o++)g=t[o],h.push([d.getNodeValue(g.cells[e]),g]);for(j?h.reverse():h.sort(f.compare),u=[],p=0,s=h.length;s>p;p++)i=h[p],u.push(l.appendChild(i[1]));return u})},getColumnType:function(a,b){var e,f,g,h,i;for(i=a.tBodies[0].rows,g=0,h=i.length;h>g;g++)if(e=i[g],f=d.getNodeValue(e.cells[b]),""!==f&&f.match(c))return d.types.numeric;return d.types.alpha},getNodeValue:function(a){return a?null!==a.getAttribute("data-value")?a.getAttribute("data-value"):"undefined"!=typeof a.innerText?a.innerText.replace(f,""):a.textContent.replace(f,""):""},types:{numeric:{defaultSortDirection:"descending",compare:function(a,b){var c,d;return c=parseFloat(a[0].replace(/[^0-9.-]/g,"")),d=parseFloat(b[0].replace(/[^0-9.-]/g,"")),isNaN(c)&&(c=0),isNaN(d)&&(d=0),d-c}},alpha:{defaultSortDirection:"ascending",compare:function(a,b){var c,d;return c=a[0].toLowerCase(),d=b[0].toLowerCase(),c===d?0:d>c?-1:1}}}},setTimeout(d.init,0),window.Sortable=d}).call(this);
\ No newline at end of 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 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
......
/**
* 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
......
/**
* 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 nl.lumc.sasc.biopet.utils.config.Configurable
......
/**
* 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 nl.lumc.sasc.biopet.FullVersion
......
/**
* 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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