Mercurial > repos > peterjc > blast2go
comparison tools/blast2go/README.rst @ 8:e23b621eb7bb draft
Uploaded v0.0.9, embed citation, updated README
author | peterjc |
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date | Thu, 26 Mar 2015 11:15:22 -0400 |
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1 Galaxy wrapper for Blast2GO for pipelines, b2g4pipe | |
2 =================================================== | |
3 | |
4 This wrapper is copyright 2011-2014 by Peter Cock, The James Hutton Institute | |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
6 See the licence text below (MIT licence). | |
7 | |
8 This is a wrapper for the command line Java tool b2g4pipe v2.5, Blast2GO for | |
9 pipelines, currently a free to use download available at: | |
10 http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip | |
11 | |
12 Note that this has been superceded by a non-free "Blast2GO Command Line (CLI)": | |
13 http://www.blast2go.com/blast2gocli/ | |
14 | |
15 This wrapper is freely available from the Galaxy Tool Shed at: | |
16 http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go | |
17 | |
18 | |
19 References | |
20 ========== | |
21 | |
22 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). | |
23 Galaxy tools and workflows for sequence analysis with applications | |
24 in molecular plant pathology. PeerJ 1:e167 | |
25 http://dx.doi.org/10.7717/peerj.167 | |
26 | |
27 S. Geotz et al. (2008). | |
28 High-throughput functional annotation and data mining with the Blast2GO suite. | |
29 Nucleic Acids Res. 36(10):3420-3435. | |
30 http://dx.doi.org/10.1093/nar/gkn176 | |
31 | |
32 A. Conesa and S. Geotz (2008). | |
33 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. | |
34 International Journal of Plant Genomics. 619832. | |
35 http://dx.doi.org/10.1155/2008/619832 | |
36 | |
37 A. Conesa et al. (2005). | |
38 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. | |
39 Bioinformatics 21:3674-3676. | |
40 http://dx.doi.org/10.1093/bioinformatics/bti610 | |
41 | |
42 See also http://www.blast2go.com/ | |
43 | |
44 | |
45 Automated Installation | |
46 ====================== | |
47 | |
48 Installation via the Galaxy Tool Shed should take care of the Galaxy side of | |
49 things, including the dependency on 'blast_datatypes' which defines the | |
50 'blastxml' file format. However, you will also probably need to configure | |
51 the Blast2GO property file(s), for example if you have a local Blast2GO | |
52 database (which we recommend for speed). | |
53 | |
54 | |
55 Manual Installation | |
56 =================== | |
57 | |
58 The main dependency is b2g4pipe which must be installed manually. Also we | |
59 strongly recommend installing a local Blast2GO database as well (see the | |
60 intructions below about the ``blast2go.loc`` file). At the time of writing, | |
61 the last free version is b2g4pipe v2.5 which is available here: | |
62 | |
63 * http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip | |
64 | |
65 You can change the path by setting the B2G4PIPE environement variable to | |
66 the desired folder, but by default the script looks for the JAR file here:: | |
67 | |
68 /opt/b2g4pipe_v2.5/blast2go.jar | |
69 | |
70 To install the wrapper manually, first install 'blast_datatypes', then | |
71 copy or move the following files under the Galaxy tools folder, e.g. in a | |
72 tools/blast2go/ folder: | |
73 | |
74 * blast2go.xml (the Galaxy tool definition) | |
75 * blast2go.py (the Python wrapper script) | |
76 * massage_xml_for_blast2go.py (Python XML reformatting script) | |
77 * README.rst (this file) | |
78 | |
79 For a manual installation of the wrapper you will also need to modify the | |
80 tools_conf.xml file to tell Galaxy to offer the tool. We suggest putting | |
81 it next to the NCBI BLAST+ wrappers. Just add the line:: | |
82 | |
83 <tool file="blast2go/blast2go.xml" /> | |
84 | |
85 If you wish to run the unit tests, also add this to tools_conf.xml.sample | |
86 and move/copy the test-data files under Galaxy's test-data folder. Then:: | |
87 | |
88 $ ./run_functional_tests.sh -id blast2go | |
89 | |
90 | |
91 Configuration | |
92 ============= | |
93 | |
94 As part of setting up b2g4pipe you will need to setup one or more Blast2GO | |
95 property files which tell the tool which database to use etc. The example | |
96 ``b2gPipe.properties`` provided with b2g4pipe is now out of date. The current | |
97 server IP address and database name may given on the Blast2GO website, or | |
98 can be found by running the latest GUI version via Java web-start, and | |
99 looking under the tools/options menu. These property files can be anywhere | |
100 accessable to the Galaxy Unix user, we put them with the JAR file etc. | |
101 | |
102 You must tell Galaxy about these Blast2GO property files so that they can | |
103 be offered to the user. Copy file ``blast2go.loc.sample`` to | |
104 ``tool-data/blast2go.loc`` under the Galaxy folder and edit this to match | |
105 your installation. This must be plain text, tab separated, with three columns: | |
106 | |
107 1. ID for the setup, e.g. ``Spain_2012_August`` | |
108 2. Description for the setup, e.g. ``Database in Spain (August 2012)`` | |
109 3. Properties filename for the setup, e.g. ``Spain_2012_August.properties`` | |
110 relative to the main JAR file, or with a full path | |
111 e.g. ``/opt/b2g4pipe/Spain_2012_August.properties`` | |
112 | |
113 Avoid including "Blast2GO" in the description (column 2) as this text will be | |
114 included in the automatically assigned output dataset name. The ``blast2go.loc`` | |
115 file allows you to customise the database setup. If for example you have a local | |
116 Blast2GO server running (which we recommend for speed), and you want this to be | |
117 the default setting, include it as the first line in your ``blast2go.loc`` file. | |
118 | |
119 Consult the Blast2GO documentation for details about the property files and | |
120 setting up a local MySQL Blast2GO database. e.g. | |
121 https://www.blast2go.com/b2gsupport/resources/35-localb2gdb | |
122 | |
123 | |
124 | |
125 History | |
126 ======= | |
127 | |
128 ======= ====================================================================== | |
129 Version Changes | |
130 ------- ---------------------------------------------------------------------- | |
131 v0.0.1 - Initial public release | |
132 v0.0.2 - Documentation clarifications, e.g. concatenated BLAST XML is allowed. | |
133 - Fixed error handler in wrapper script (for when b2g4pipe fails). | |
134 - Reformats the XML to use old NCBI-style concatenated BLAST XML since | |
135 b2g4pipe crashes with heap space error on with large files using | |
136 current NCBI output. | |
137 v0.0.3 - Include sample loc file, ``tool-data/blast2go.loc.sample`` | |
138 v0.0.4 - Include ``repository_dependencies.xml`` file for ``blastxml`` format | |
139 (previously included in the core Galaxy installation) | |
140 v0.0.5 - Quote arguments in case of spaces in filenames (internal change) | |
141 - Last release supporting b2g4pipe v2.3.5 | |
142 v0.0.6 - Support for b2g4pipe v2.5 instead of v2.3.5 | |
143 | |
144 - Now invoked with a class path and es.blast2go.prog.B2GAnnotPipe | |
145 rather then simply calling the jar file | |
146 - Now uses the switch ``-annot`` instead of ``-a`` (this change | |
147 breaks support for b2g4pipe v2.3.5 unfortunately) | |
148 | |
149 - Catch a few error messages and treat them explicitly as errors. | |
150 v0.0.7 - Update output description in XML file (b2g4pipe v2.3.5 included | |
151 the sequence description, b2g4pipe v2.5 omits this). | |
152 v0.0.8 - Automated installation via the Galaxy Tool Shed. | |
153 - Added unit test. | |
154 - Explain how to load the tabular file into the Blast2GO GUI. | |
155 - Link to Tool Shed added to help text and this documentation. | |
156 - Switch to standard MIT licence. | |
157 - Use reStructuredText for this README file. | |
158 - Updated citation information (Cock et al. 2013). | |
159 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast | |
160 - Split out ``massage_xml_for_blast2go.py`` as a standalone file. | |
161 v0.0.9 - Update README file now that BioBam are selling the latest version | |
162 of the Blast2GO command line tool. For now b2g4pipe v2.5 is still | |
163 available as a free download. | |
164 - Tool definition now embeds citation information. | |
165 ======= ====================================================================== | |
166 | |
167 | |
168 Developers | |
169 ========== | |
170 | |
171 This script and related tools were originally developed on the 'tools' branch | |
172 of the following BitBucket Mercurial repository: | |
173 https://bitbucket.org/peterjc/galaxy-central/ | |
174 | |
175 As of September 2013, development is continuing on a dedicated GitHub repository: | |
176 https://github.com/peterjc/galaxy_blast | |
177 | |
178 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
179 the following command from the Galaxy root folder:: | |
180 | |
181 $ tar -czf blast2go.tar.gz tools/blast2go/README.rst tools/blast2go/blast2go.xml tools/blast2go/blast2go.py tools/blast2go/massage_xml_for_blast2go.py tools/blast2go/repository_dependencies.xml tools/blast2go/tool_dependencies.xml tool-data/blast2go.loc.sample test-data/blastp_sample.xml test-data/blastp_sample.blast2go.tabular | |
182 | |
183 Check this worked:: | |
184 | |
185 $ tar -tzf blast2go.tar.gz | |
186 tools/blast2go/README.rst | |
187 tools/blast2go/blast2go.xml | |
188 tools/blast2go/blast2go.py | |
189 tools/blast2go/massage_xml_for_blast2go.py | |
190 tools/blast2go/repository_dependencies.xml | |
191 tools/blast2go/tool_dependencies.xml | |
192 tool-data/blast2go.loc.sample | |
193 test-data/blastp_sample.xml | |
194 test-data/blastp_sample.blast2go.tabular | |
195 | |
196 | |
197 Licence (MIT) | |
198 ============= | |
199 | |
200 Permission is hereby granted, free of charge, to any person obtaining a copy | |
201 of this software and associated documentation files (the "Software"), to deal | |
202 in the Software without restriction, including without limitation the rights | |
203 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
204 copies of the Software, and to permit persons to whom the Software is | |
205 furnished to do so, subject to the following conditions: | |
206 | |
207 The above copyright notice and this permission notice shall be included in | |
208 all copies or substantial portions of the Software. | |
209 | |
210 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
211 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
212 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
213 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
214 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
215 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
216 THE SOFTWARE. | |
217 | |
218 | |
219 NOTE: This is the licence for the Galaxy Wrapper only. Blast2GO and | |
220 associated data files are available and licenced separately. |