Mercurial > repos > crs4 > kggseq_variant_selection

comparison tool_dependencies.xml @ 0:d388273fb83f draft

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author crs4
date Fri, 12 Sep 2014 21:40:16 -0400
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children e9758eee6697
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="kggseq" version="0.4_20140910">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url" target_filename="kggseq_archive-0.4_20140910.tar.gz">https://github.com/nsoranzo/kggseq_archive/archive/v0.4_20140910.tar.gz</action>
7 <action type="shell_command">touch test.vcf</action>
8 <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter hg19_1kg201305,hg19_1kg201204,hg19_ESP6500AA,hg19_ESP6500EA,hg19_dbsnp141,hg19_dbsnp138,hg19_dbsnp137 --genome-annot --db-gene refgene,gencode,knowngene --db-score dbnsfp --superdup-annot --vcf-file test.vcf</action>
9 <action type="move_directory_files">
10 <source_directory>.</source_directory>
11 <destination_directory>$INSTALL_DIR</destination_directory>
12 </action>
13 <action type="set_environment">
14 <environment_variable name="KGGSEQ_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
15 </action>
16 </actions>
17 </install>
18 </package>
19 </tool_dependency>