|
0
|
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 This is the last version of BWA that uses separate files for BWT and reverse BWT.
|
|
|
19
|
|
|
20 Program: bwa (alignment via Burrows-Wheeler transformation)
|
|
|
21 Version: 0.5.9-r16
|
|
|
22 Contact: Heng Li <lh3@sanger.ac.uk>
|
|
|
23
|
|
|
24 Usage: bwa <command> [options]
|
|
|
25
|
|
|
26 Command: index index sequences in the FASTA format
|
|
|
27 aln gapped/ungapped alignment
|
|
|
28 samse generate alignment (single ended)
|
|
|
29 sampe generate alignment (paired ended)
|
|
|
30 bwasw BWA-SW for long queries
|
|
|
31
|
|
|
32 fa2pac convert FASTA to PAC format
|
|
|
33 pac2bwt generate BWT from PAC
|
|
|
34 pac2bwtgen alternative algorithm for generating BWT
|
|
|
35 bwtupdate update .bwt to the new format
|
|
|
36 pac_rev generate reverse PAC
|
|
|
37 bwt2sa generate SA from BWT and Occ
|
|
|
38 pac2cspac convert PAC to color-space PAC
|
|
|
39 stdsw standard SW/NW alignment
|
|
|
40 </readme>
|
|
|
41 </package>
|
|
|
42 </tool_dependency> |
