Mercurial > repos > devteam > package_bwa_0_5_9

annotate tool_dependencies.xml @ 2:90168f400592 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix download link for mac / darwin
author devteam
date Wed, 09 Apr 2014 09:07:13 -0400
parents 1e8ba0ebe119
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
2 <tool_dependency>
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
3 <package name="bwa" version="0.5.9">
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
4 <install version="1.0">
1
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
5 <actions_group>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
6 <actions architecture="i386" os="linux">
1e8ba0ebe119 Uploaded updated tool dependency definition with 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>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
8 <action type="move_directory_files">
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
9 <source_directory>.</source_directory>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
11 </action>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
12 </actions>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
13 <actions architecture="x86_64" os="linux">
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bwa/bwa-0.5.9-Linux-x86_64.tgz</action>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
15 <action type="move_directory_files">
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
16 <source_directory>.</source_directory>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
18 </action>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
19 </actions>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
20 <actions architecture="x86_64" os="darwin">
2
90168f400592 Fix download link for mac / darwin
devteam
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
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
22 <action type="move_directory_files">
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
23 <source_directory>.</source_directory>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
24 <destination_directory>$INSTALL_DIR/bin</destination_directory>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
25 </action>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
26 </actions>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
27 <actions>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
28 <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
29 <action type="shell_command">make</action>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
30 <action type="move_file">
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
31 <source>bwa</source>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
32 <destination>$INSTALL_DIR/bin</destination>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
33 </action>
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
34 </actions>
0
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
35 <action type="set_environment">
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
37 </action>
1
1e8ba0ebe119 Uploaded updated tool dependency definition with precompiled binaries.
devteam
parents: 0
diff changeset
38 </actions_group>
0
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
39 </install>
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
40 <readme>
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
41 This is the last version of BWA that uses separate files for BWT and reverse BWT.
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
42
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
43 Program: bwa (alignment via Burrows-Wheeler transformation)
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
44 Version: 0.5.9-r16
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
45 Contact: Heng Li &lt;lh3@sanger.ac.uk&gt;
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
46
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
47 Usage: bwa &lt;command&gt; [options]
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
48
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
49 Command: index index sequences in the FASTA format
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
50 aln gapped/ungapped alignment
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
51 samse generate alignment (single ended)
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
52 sampe generate alignment (paired ended)
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
53 bwasw BWA-SW for long queries
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
54
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
55 fa2pac convert FASTA to PAC format
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
56 pac2bwt generate BWT from PAC
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
57 pac2bwtgen alternative algorithm for generating BWT
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
58 bwtupdate update .bwt to the new format
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
59 pac_rev generate reverse PAC
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
60 bwt2sa generate SA from BWT and Occ
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
61 pac2cspac convert PAC to color-space PAC
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
62 stdsw standard SW/NW alignment
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
63 </readme>
f59e468f1964 Uploaded tool_dependencies.xml
devteam
parents:
diff changeset
64 </package>
2
90168f400592 Fix download link for mac / darwin
devteam
parents: 1
diff changeset
65 </tool_dependency>