Mercurial > repos > cjav > package_bwa_0_7_5a
changeset 0:df10a1254304 draft default tip
Uploaded
| author | cjav |
|---|---|
| date | Tue, 24 Sep 2013 13:09:58 -0400 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 40 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Sep 24 13:09:58 2013 -0400 @@ -0,0 +1,40 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bwa" version="0.7.5a"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.5a.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> +Program: bwa (alignment via Burrows-Wheeler transformation) +Version: 0.7.5a-r405 +Contact: Heng Li <lh3@sanger.ac.uk> + +Usage: bwa <command> [options] + +Command: index index sequences in the FASTA format + mem BWA-MEM algorithm + fastmap identify super-maximal exact matches + pemerge merge overlapping paired ends (EXPERIMENTAL) + 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 + bwt2sa generate SA from BWT and Occ + </readme> + </package> +</tool_dependency>