Mercurial > repos > crs4 > kggseq_variant_selection
comparison tool_dependencies.xml @ 3:c758125c56d8 draft
Update to KggSeq release 0.8 (23/Apr./2015)
| author | crs4 |
|---|---|
| date | Mon, 25 May 2015 18:01:25 -0400 |
| parents | e9758eee6697 |
| children | a13b8ff61c6c |
comparison
equal
deleted
inserted
replaced
| 2:e1a21c2f4997 | 3:c758125c56d8 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="kggseq" version="0.7_20150118"> | 3 <package name="kggseq" version="0.8_20150423"> |
| 4 <install version="1.0"> | 4 <install version="1.0"> |
| 5 <actions> | 5 <actions> |
| 6 <action type="download_by_url" target_filename="kggseq_archive-0.7_20150118.tar.gz">https://github.com/crs4/kggseq_archive/archive/v0.7_20150118.tar.gz</action> | 6 <action type="download_by_url" target_filename="kggseq_archive-v0.8_20150423.tar.gz">https://github.com/crs4/kggseq_archive/archive/v0.8_20150423.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 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> | 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="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> |
| 10 <action type="move_directory_files"> | 10 <action type="move_directory_files"> |
| 11 <source_directory>.</source_directory> | 11 <source_directory>.</source_directory> |