Mercurial > repos > crs4 > kggseq_variant_selection

comparison tool_dependencies.xml @ 0:211c12415e48 draft

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author crs4
date Mon, 18 Apr 2016 05:15:13 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="kggseq" version="1.0_0_20160412">
4 <install version="1.0">
5 <actions>
6 <action type="download_by_url" target_filename="kggseq_archive-v1.0_20160412.tar.gz">https://github.com/crs4/kggseq_archive/archive/v1.0_20160412.tar.gz</action>
7 <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kgeur201305,1kgeas201305,1kgafr201305,1kgsas201305,1kgamr201305,1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all --patho-gene-predict --dgv-cnv-annot --o-flanking-seq 10 --vcf-file examples-lite/rare.disease.hg19.vcf</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 <action type="set_environment">
13 <environment_variable name="KGGSEQ_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
14 </action>
15 </actions>
16 </install>
17 </package>
18 </tool_dependency>