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1 Galaxy tool to find BLAST Reciprocal Best Hits (RBH)
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2 ====================================================
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3
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4 This tool 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.
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7
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8 This tool is a short Python script to run reciprocal BLAST searches on a
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9 pair of sequence files, and extract the reciprocal best hits.
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10
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11 This is a work in progress, and builds on an earlier implementation which
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12 prequired the two BLAST searches be prepared in advance. Integration allows
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13 a much simpler user experience, and can ensure sensible filters are used.
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14
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15
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16 Automated Installation
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17 ======================
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18
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19 Installation via the Galaxy Tool Shed should take care of the Galaxy side of
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20 things, including the dependency the NCBI BLAST+ binaries.
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21
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22
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23 Manual Installation
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24 ===================
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25
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26 There are just two files to install:
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27
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28 - ``blast_rbh.py`` (the Python script)
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29 - ``blast_rbh.xml`` (the Galaxy tool definition)
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30
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31 The suggested location is in a ``tools/blast_rbh/`` folder. You will then
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32 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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33 by adding the line::
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34
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35 <tool file="blast_rbh/blast_rbh.xml" />
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36
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37 If you want to run the functional tests, include the same line in your
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38 ``tool_conf.xml.sample`` file, and the sample test files under Galaxy's
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39 ``test-data/`` directory. Then::
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40
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41 ./run_functional_tests.sh -id blast_reciprocal_best_hits
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42
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43 You will need to have the NCBI BLAST+ binaries installed and on the ``$PATH``.
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44
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45
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46 History
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47 =======
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48
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49 ======= ======================================================================
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50 Version Changes
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51 ------- ----------------------------------------------------------------------
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52 v0.1.0 - Initial public release, targetting NCBI BLAST+ 2.2.29
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53 ======= ======================================================================
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54
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55
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56 Developers
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57 ==========
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58
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59 This tool is developed on the following GitHub repository:
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60 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
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61
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62 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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63 the following command from the Galaxy root folder::
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64
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65 $ tar -czf blast_rbh.tar.gz tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml tools/blast_rbh/blast_rbh.py tools/blast_rbh/repository_dependencies.xml test-data/rhodopsin_nucs.fasta test-data/rhodopsin_proteins.fasta test-data/three_human_mRNA.fasta test-data/four_human_proteins.fasta test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular test-data/rbh_none.tabular
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66
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67 Check this worked::
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68
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69 $ tar -tzf blast_rbh.tar.gz
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70 tools/blast_rbh/README.rst
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71 tools/blast_rbh/blast_rbh.xml
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72 tools/blast_rbh/blast_rbh.py
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73 tools/blast_rbh/repository_dependencies.xml
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74 test-data/rhodopsin_nucs.fasta
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75 test-data/rhodopsin_proteins.fasta
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76 test-data/three_human_mRNA.fasta
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77 test-data/four_human_proteins.fasta
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78 test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular
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79 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
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80 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular
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81 test-data/rbh_none.tabular
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82
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83
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84 Licence (MIT)
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85 =============
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86
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87 Permission is hereby granted, free of charge, to any person obtaining a copy
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88 of this software and associated documentation files (the "Software"), to deal
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89 in the Software without restriction, including without limitation the rights
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90 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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91 copies of the Software, and to permit persons to whom the Software is
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92 furnished to do so, subject to the following conditions:
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93
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94 The above copyright notice and this permission notice shall be included in
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95 all copies or substantial portions of the Software.
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96
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97 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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98 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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99 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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100 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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101 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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102 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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103 THE SOFTWARE.
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