Mercurial > repos > crs4 > kggseq_variant_selection
diff tool_dependencies.xml @ 1:e9758eee6697 draft
Update to KggSeq v0.7_20150118
author | crs4 |
---|---|
date | Tue, 28 Apr 2015 04:42:14 -0400 |
parents | d388273fb83f |
children | c758125c56d8 |
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--- a/tool_dependencies.xml Fri Sep 12 21:40:16 2014 -0400 +++ b/tool_dependencies.xml Tue Apr 28 04:42:14 2015 -0400 @@ -1,11 +1,12 @@ <?xml version="1.0"?> <tool_dependency> - <package name="kggseq" version="0.4_20140910"> + <package name="kggseq" version="0.7_20150118"> <install version="1.0"> <actions> - <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> + <action type="download_by_url" target_filename="kggseq_archive-0.7_20150118.tar.gz">https://github.com/crs4/kggseq_archive/archive/v0.7_20150118.tar.gz</action> <action type="shell_command">touch test.vcf</action> - <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> + <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 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 --vcf-file test.vcf</action> + <action type="shell_command">java -Xmx4g -jar kggseq.jar --no-lib-check --no-qc --resource resources --buildver hg19 --o-flanking-seq 10 --vcf-file examples/rare.disease.hg19.vcf</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory>