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annotate tools/ncbi_blast_plus/blast2go.txt @ 1:0f159cf346c8

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Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 16:29:28 -0400
parents cd52c931b325
children e88a3246520e
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cd52c931b325 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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1 Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
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2 ===================================================
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3
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4 This wrapper is copyright 2011 by Peter Cock, The James Hutton Institute
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
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6 See the licence text below.
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7
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8 This is a wrapper for the command line Java tool b2g4pipe v2.3.5,
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9 Blast2GO for pipelines. See:
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10
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11 S. Götz et al.
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12 High-throughput functional annotation and data mining with the Blast2GO suite.
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13 Nucleic Acids Res. 36(10):3420–3435, 2008.
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14 http://dx.doi.org/10.1093/nar/gkn176
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15
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16 A. Conesa and S. Götz.
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17 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
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18 Int. J. Plant Genomics. 619832, 2008.
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19 http://dx.doi.org/10.1155/2008/619832
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20
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21 A. Conesa et al.
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22 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
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23 Bioinformatics 21:3674-3676, 2005.
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24 http://dx.doi.org/10.1093/bioinformatics/bti610
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25
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26 http://www.blast2go.org/
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29
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30 Installation
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31 ============
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32
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33 You can change the path by editing the definition near the start of the Python
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34 script blast2go.py, but by default it expects the underlying tool to be here:
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35
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36 /opt/b2g4pip/blast2go.jar
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37
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38 To install the wrapper copy or move the following files under the Galaxy tools
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39 folder, e.g. in the tools/ncbi_blast_blast folder:
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40
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41 * blast2go.xml (the Galaxy tool definition)
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42 * blast2go.py (the Python wrapper script)
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43 * blast2go.txt (this README file)
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44
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45 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
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46 tool. We suggest putting it next to the NCBI BLAST+ wrappers. Just add the line:
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47
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48 <tool file="ncbi_blast_plus/blast2go.xml" />
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49
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50 As part of setting up b2g4pipe you will need to setup one or more Blast2GO
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51 property files which tell the tool which database to use etc. The example
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52 b2gPipe.properties provided with b2g4pipe v2.3.5 is out of date, with the
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53 latest server IP address and database name given on the Blast2GO website.
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54 These files can be anywhere accessable to the Galaxy Unix user, we put them
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55 under /opt/b2g4pipe with the JAR file etc.
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56
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57 You must tell Galaxy about these Blast2GO property files so that they can be
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58 offered to the user. Create the file tool-data/blast2go.loc under the Galaxy
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59 folder. This must be plain text, tab separated, with three columns:
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60
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61 (1) ID for the setup, e.g. Spain_2010_May
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62 (2) Description for the setup, e.g. Database in Spain (May 2010)
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63 (3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2010_May.properties
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64
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65 Avoid including "Blast2GO" in the description (column 2) as this will be
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66 included in the automatically assigned output dataset name. The blast2go.loc
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67 file allows you to customise the database setup. If for example you have a local
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68 Blast2GO server running (which we recommend for speed), and you want this to be
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69 the default setting, include it as the first line in your blast2go.loc file.
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70
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71 Consult the Blast2GO documentation for details about the property files and
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72 setting up a local MySQL Blast2GO database.
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75 History
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76 =======
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77
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78 v0.0.1 - Initial public release
1
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79 v0.0.2 - Documentation clarifications, e.g. concatenated BLAST XML is allowed.
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80 - Fixed error handler in wrapper script (for when b2g4pipe fails).
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81 - Reformats the XML to use old NCBI-style concatenated BLAST XML since
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82 b2g4pipe crashes with heap space error on with large files using
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83 current NCBI output.
0
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85
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86 Developers
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87 ==========
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88
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89 This script and related tools are being developed on the following hg branch:
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90 http://bitbucket.org/peterjc/galaxy-central/src/tools
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91
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92 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use
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93 the following command from the Galaxy root folder:
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94
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95 $ tar -czf blast2go.tar.gz tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt
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96
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97 Check this worked:
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98
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99 $ tar -tzf blast2go.tar.gz
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100 tools/ncbi_blast_plus/blast2go.xml
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101 tools/ncbi_blast_plus/blast2go.py
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102 tools/ncbi_blast_plus/blast2go.txt
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104
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105 Licence (MIT/BSD style)
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106 =======================
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107
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108 Permission to use, copy, modify, and distribute this software and its
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109 documentation with or without modifications and for any purpose and
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110 without fee is hereby granted, provided that any copyright notices
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111 appear in all copies and that both those copyright notices and this
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112 permission notice appear in supporting documentation, and that the
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113 names of the contributors or copyright holders not be used in
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114 advertising or publicity pertaining to distribution of the software
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115 without specific prior permission.
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116
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117 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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118 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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119 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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120 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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121 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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122 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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123 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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124 OR PERFORMANCE OF THIS SOFTWARE.
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125
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126 NOTE: This is the licence for the Galaxy Wrapper only. Blast2GO and
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127 associated data files are available and licenced separately.