Commit 3b313f12 authored by Peter van 't Hof's avatar Peter van 't Hof

Move tool extensions inside the core

parent 2f0ebca5
......@@ -39,7 +39,7 @@
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
......
......@@ -35,6 +35,11 @@
<artifactId>BiopetUtils</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetTools</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue</artifactId>
......
<?xml version="1.0" encoding="UTF-8"?>
<!--
Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
-->
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>Biopet</artifactId>
<groupId>nl.lumc.sasc</groupId>
<version>0.10.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>BiopetToolsExtensions</artifactId>
<dependencies>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetCore</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetTools</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file
......@@ -39,7 +39,7 @@
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
......
......@@ -44,7 +44,7 @@
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
......
......@@ -85,7 +85,8 @@ class DownloadGenomes(val parent: Configurable) extends QScript with BiopetQScri
val ncbiReportToContigMap = new NcbiReportToContigMap(this)
ncbiReportToContigMap.assemblyReport = ncbiAssemblyReport
ncbiReportToContigMap.contigMap = new File(genomeDir, s"${speciesName}-${genomeName}.contig.map.tsv")
ncbiReportToContigMap.contigMap =
new File(genomeDir, s"${speciesName}-${genomeName}.contig.map.tsv")
ncbiReportToContigMap.nameHeader = genomeConfig
.get("ncbi_assembly_header_name")
.map(_.toString)
......
......@@ -42,10 +42,5 @@
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>
......@@ -43,7 +43,6 @@
<module>biopet-core</module>
<module>biopet-utils</module>
<module>biopet-tools</module>
<module>biopet-tools-extensions</module>
<module>biopet-extensions</module>
<module>biopet-tools-package</module>
<module>gwas-test</module>
......
......@@ -39,7 +39,7 @@
</dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId>
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
......
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