annotate tool_dependencies.xml @ 2:ec2595e4d313 default tip

Fix download link for mac / darwin
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 14 Feb 2014 13:16:06 -0500
parents 0eb3d3c40344
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
2 <tool_dependency>
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
3 <package name="bwa" version="0.5.9">
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
4 <install version="1.0">
1
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
5 <actions_group>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
6 <actions architecture="i386" os="linux">
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/bwa/bwa-0.5.9-Linux-i686.tgz</action>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
8 <action type="move_directory_files">
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
9 <source_directory>.</source_directory>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
11 </action>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
12 </actions>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
13 <actions architecture="x86_64" os="linux">
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bwa/bwa-0.5.9-Linux-x86_64.tgz</action>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
15 <action type="move_directory_files">
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
16 <source_directory>.</source_directory>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
18 </action>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
19 </actions>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
20 <actions architecture="x86_64" os="darwin">
2
ec2595e4d313 Fix download link for mac / darwin
Daniel Blankenberg <dan@bx.psu.edu>
parents: 1
diff changeset
21 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/bwa/bwa-0.5.9-Darwin-x86_64.tgz</action>
1
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
22 <action type="move_directory_files">
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
23 <source_directory>.</source_directory>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
24 <destination_directory>$INSTALL_DIR/bin</destination_directory>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
25 </action>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
26 </actions>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
27 <actions>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
28 <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
29 <action type="shell_command">make</action>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
30 <action type="move_file">
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
31 <source>bwa</source>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
32 <destination>$INSTALL_DIR/bin</destination>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
33 </action>
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
34 </actions>
0
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
35 <action type="set_environment">
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
37 </action>
1
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
38 </actions_group>
0
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
39 </install>
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
40 <readme>
1
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
41 This is the last version of BWA that uses separate files for BWT and reverse BWT.
0eb3d3c40344 Uploaded updated tool dependency definition specifiying precompiled binaries.
devteam
parents: 0
diff changeset
42
0
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
43 Program: bwa (alignment via Burrows-Wheeler transformation)
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
44 Version: 0.5.9-r16
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
45 Contact: Heng Li &lt;lh3@sanger.ac.uk&gt;
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
46
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
47 Usage: bwa &lt;command&gt; [options]
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
48
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
49 Command: index index sequences in the FASTA format
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
50 aln gapped/ungapped alignment
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
51 samse generate alignment (single ended)
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
52 sampe generate alignment (paired ended)
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
53 bwasw BWA-SW for long queries
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
54
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
55 fa2pac convert FASTA to PAC format
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
56 pac2bwt generate BWT from PAC
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
57 pac2bwtgen alternative algorithm for generating BWT
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
58 bwtupdate update .bwt to the new format
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
59 pac_rev generate reverse PAC
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
60 bwt2sa generate SA from BWT and Occ
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
61 pac2cspac convert PAC to color-space PAC
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
62 stdsw standard SW/NW alignment
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
63 </readme>
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
64 </package>
7959322e3f4b Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
65 </tool_dependency>