Mercurial > repos > devteam > package_bwa_0_5_9
comparison tool_dependencies.xml @ 0:7959322e3f4b
Uploaded tool_dependencies.xml
| author | devteam |
|---|---|
| date | Tue, 05 Feb 2013 14:15:40 -0500 |
| parents | |
| children | 0eb3d3c40344 |
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| -1:000000000000 | 0:7959322e3f4b |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="bwa" version="0.5.9"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> | |
| 7 <action type="shell_command">make</action> | |
| 8 <action type="move_file"> | |
| 9 <source>bwa</source> | |
| 10 <destination>$INSTALL_DIR/bin</destination> | |
| 11 </action> | |
| 12 <action type="set_environment"> | |
| 13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 14 </action> | |
| 15 </actions> | |
| 16 </install> | |
| 17 <readme> | |
| 18 Program: bwa (alignment via Burrows-Wheeler transformation) | |
| 19 Version: 0.5.9-r16 | |
| 20 Contact: Heng Li <lh3@sanger.ac.uk> | |
| 21 | |
| 22 Usage: bwa <command> [options] | |
| 23 | |
| 24 Command: index index sequences in the FASTA format | |
| 25 aln gapped/ungapped alignment | |
| 26 samse generate alignment (single ended) | |
| 27 sampe generate alignment (paired ended) | |
| 28 bwasw BWA-SW for long queries | |
| 29 | |
| 30 fa2pac convert FASTA to PAC format | |
| 31 pac2bwt generate BWT from PAC | |
| 32 pac2bwtgen alternative algorithm for generating BWT | |
| 33 bwtupdate update .bwt to the new format | |
| 34 pac_rev generate reverse PAC | |
| 35 bwt2sa generate SA from BWT and Occ | |
| 36 pac2cspac convert PAC to color-space PAC | |
| 37 stdsw standard SW/NW alignment | |
| 38 </readme> | |
| 39 </package> | |
| 40 </tool_dependency> |