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12 Note that this has been superceded by a non-free "Blast2GO Command Line (CLI)":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