Mercurial > repos > crs4 > kggseq_variant_selection
comparison 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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| 0:d388273fb83f | 1:e9758eee6697 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="kggseq" version="0.4_20140910"> | 3 <package name="kggseq" version="0.7_20150118"> |
| 4 <install version="1.0"> | 4 <install version="1.0"> |
| 5 <actions> | 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> | 6 <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> |
| 7 <action type="shell_command">touch test.vcf</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> | 8 <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> |
| 9 <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> | |
| 9 <action type="move_directory_files"> | 10 <action type="move_directory_files"> |
| 10 <source_directory>.</source_directory> | 11 <source_directory>.</source_directory> |
| 11 <destination_directory>$INSTALL_DIR</destination_directory> | 12 <destination_directory>$INSTALL_DIR</destination_directory> |
| 12 </action> | 13 </action> |
| 13 <action type="set_environment"> | 14 <action type="set_environment"> |