Mercurial > repos > peterjc > blast2go

comparison tools/ncbi_blast_plus/blast2go.txt @ 0:cd52c931b325

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 16:28:31 -0400
parents
children 0f159cf346c8
comparison
equal deleted inserted replaced
-1:000000000000 0:cd52c931b325
1 Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
2 ===================================================
3
4 This wrapper is copyright 2011 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below.
7
8 This is a wrapper for the command line Java tool b2g4pipe v2.3.5,
9 Blast2GO for pipelines. See:
10
11 S. Götz et al.
12 High-throughput functional annotation and data mining with the Blast2GO suite.
13 Nucleic Acids Res. 36(10):3420–3435, 2008.
14 http://dx.doi.org/10.1093/nar/gkn176
15
16 A. Conesa and S. Götz.
17 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
18 Int. J. Plant Genomics. 619832, 2008.
19 http://dx.doi.org/10.1155/2008/619832
20
21 A. Conesa et al.
22 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
23 Bioinformatics 21:3674-3676, 2005.
24 http://dx.doi.org/10.1093/bioinformatics/bti610
25
26 http://www.blast2go.org/
27
28
29
30 Installation
31 ============
32
33 You can change the path by editing the definition near the start of the Python
34 script blast2go.py, but by default it expects the underlying tool to be here:
35
36 /opt/b2g4pip/blast2go.jar
37
38 To install the wrapper copy or move the following files under the Galaxy tools
39 folder, e.g. in the tools/ncbi_blast_blast folder:
40
41 * blast2go.xml (the Galaxy tool definition)
42 * blast2go.py (the Python wrapper script)
43 * blast2go.txt (this README file)
44
45 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
46 tool. We suggest putting it next to the NCBI BLAST+ wrappers. Just add the line:
47
48 <tool file="ncbi_blast_plus/blast2go.xml" />
49
50 As part of setting up b2g4pipe you will need to setup one or more Blast2GO
51 property files which tell the tool which database to use etc. The example
52 b2gPipe.properties provided with b2g4pipe v2.3.5 is out of date, with the
53 latest server IP address and database name given on the Blast2GO website.
54 These files can be anywhere accessable to the Galaxy Unix user, we put them
55 under /opt/b2g4pipe with the JAR file etc.
56
57 You must tell Galaxy about these Blast2GO property files so that they can be
58 offered to the user. Create the file tool-data/blast2go.loc under the Galaxy
59 folder. This must be plain text, tab separated, with three columns:
60
61 (1) ID for the setup, e.g. Spain_2010_May
62 (2) Description for the setup, e.g. Database in Spain (May 2010)
63 (3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2010_May.properties
64
65 Avoid including "Blast2GO" in the description (column 2) as this will be
66 included in the automatically assigned output dataset name. The blast2go.loc
67 file allows you to customise the database setup. If for example you have a local
68 Blast2GO server running (which we recommend for speed), and you want this to be
69 the default setting, include it as the first line in your blast2go.loc file.
70
71 Consult the Blast2GO documentation for details about the property files and
72 setting up a local MySQL Blast2GO database.
73
74
75 History
76 =======
77
78 v0.0.1 - Initial public release
79
80
81 Developers
82 ==========
83
84 This script and related tools are being developed on the following hg branch:
85 http://bitbucket.org/peterjc/galaxy-central/src/tools
86
87 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use
88 the following command from the Galaxy root folder:
89
90 $ tar -czf blast2go.tar.gz tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt
91
92 Check this worked:
93
94 $ tar -tzf blast2go.tar.gz
95 tools/ncbi_blast_plus/blast2go.xml
96 tools/ncbi_blast_plus/blast2go.py
97 tools/ncbi_blast_plus/blast2go.txt
98
99
100 Licence (MIT/BSD style)
101 =======================
102
103 Permission to use, copy, modify, and distribute this software and its
104 documentation with or without modifications and for any purpose and
105 without fee is hereby granted, provided that any copyright notices
106 appear in all copies and that both those copyright notices and this
107 permission notice appear in supporting documentation, and that the
108 names of the contributors or copyright holders not be used in
109 advertising or publicity pertaining to distribution of the software
110 without specific prior permission.
111
112 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
113 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
114 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
115 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
116 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
117 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
118 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
119 OR PERFORMANCE OF THIS SOFTWARE.
120
121 NOTE: This is the licence for the Galaxy Wrapper only. Blast2GO and
122 associated data files are available and licenced separately.