Mercurial > repos > devteam > package_bwa_0_5_9
changeset 0:f59e468f1964 draft
Uploaded tool_dependencies.xml
| author | devteam |
|---|---|
| date | Tue, 05 Feb 2013 12:56:32 -0500 |
| parents | |
| children | 1e8ba0ebe119 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 42 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Feb 05 12:56:32 2013 -0500 @@ -0,0 +1,42 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bwa" version="0.5.9"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>bwa</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +This is the last version of BWA that uses separate files for BWT and reverse BWT. + +Program: bwa (alignment via Burrows-Wheeler transformation) +Version: 0.5.9-r16 +Contact: Heng Li <lh3@sanger.ac.uk> + +Usage: bwa <command> [options] + +Command: index index sequences in the FASTA format + aln gapped/ungapped alignment + samse generate alignment (single ended) + sampe generate alignment (paired ended) + bwasw BWA-SW for long queries + + fa2pac convert FASTA to PAC format + pac2bwt generate BWT from PAC + pac2bwtgen alternative algorithm for generating BWT + bwtupdate update .bwt to the new format + pac_rev generate reverse PAC + bwt2sa generate SA from BWT and Occ + pac2cspac convert PAC to color-space PAC + stdsw standard SW/NW alignment + </readme> + </package> +</tool_dependency> \ No newline at end of file