Mercurial > repos > peterjc > blast_rbh

annotate tools/blast_rbh/README.rst @ 20:e8f8c580bcca draft

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planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast_rbh commit 05c2a834609f1fd02372c4f9b0a0733680fe9675-dirty
author peterjc
date Fri, 15 May 2015 05:47:40 -0400
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1 Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper
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2 ==========================================================
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4 This tool is copyright 2011-2015 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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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. The script
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10 ``blast_rbh.py`` can be used directly (without Galaxy) as long as NCBI
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11 BLAST+ is installed.
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13 It comes with an optional Galaxy tool definition file ``blast_rbh.xml``
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14 allowing the Python script to be run from within Galaxy. It is available
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15 from the Galaxy Tool Shed at:
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16 http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
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19 Citation
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20 ========
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21
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22 Please cite the following paper (currently available as a preprint):
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23
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24 NCBI BLAST+ integrated into Galaxy.
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25 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
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26 bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint)
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27
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28 You should also cite the NCBI BLAST+ tools:
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29
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30 BLAST+: architecture and applications.
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31 C. Camacho et al. BMC Bioinformatics 2009, 10:421.
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32 DOI: http://dx.doi.org/10.1186/1471-2105-10-421
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34
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35 Automated Installation
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36 ======================
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37
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38 Installation via the Galaxy Tool Shed should take care of the Galaxy side of
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39 things, including the dependency the NCBI BLAST+ binaries.
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40
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42 Manual Installation
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43 ===================
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44
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45 There are just two files to install:
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46
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47 - ``blast_rbh.py`` (the Python script)
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48 - ``blast_rbh.xml`` (the Galaxy tool definition)
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49
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50 The suggested location is in a ``tools/blast_rbh/`` folder. You will then
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51 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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52 by adding the line::
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53
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54 <tool file="blast_rbh/blast_rbh.xml" />
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55
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56 If you want to run the functional tests, copy the sample test files under
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57 sample test files under Galaxy's ``test-data/`` directory. Then::
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59 ./run_tests.sh -id blast_reciprocal_best_hits
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61 You will need to have the NCBI BLAST+ binaries installed and on the ``$PATH``.
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64 History
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65 =======
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66
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67 ======= ======================================================================
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68 Version Changes
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69 ------- ----------------------------------------------------------------------
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70 v0.1.0 - Initial Test Tool Shed release, targetting NCBI BLAST+ 2.2.29
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71 v0.1.1 - Supports self-comparison, sometimes useful for spotting duplicates.
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72 v0.1.2 - Using optparse for command line API.
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73 - Tool definition now embeds citation information.
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74 - Fixed Tool Shed dependency definition.
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75 v0.1.3 - Option to make FASTA files non-redundant (via Biopython dependency).
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76 - Avoid extra database and BLAST search in self-comparison mode.
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77 v0.1.4 - Check for duplicate FASTA identifiers (workaround for makeblastdb
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78 not treating this as an error, leading to confusing RBH output).
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79 v0.1.5 - Clarify documentation for using the Python script outside Galaxy.
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80 - Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install.
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81 v0.1.6 - Offer the new blastp-fast task added in BLAST+ 2.2.30.
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82 - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
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83 v0.1.7 - Reorder XML elements (internal change only).
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84 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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85 ======= ======================================================================
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88 Developers
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89 ==========
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90
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91 This tool is developed on the following GitHub repository:
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92 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
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93
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94 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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95 Planemo commands (which requires you have set your Tool Shed access details in
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96 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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98 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
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99 ...
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101 or::
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103 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
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104 ...
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106 To just build and check the tar ball, use::
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107
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108 $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/tools/blast_rbh/
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109 ...
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110 $ tar -tzf shed_upload.tar.gz
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111 test-data/four_human_proteins.fasta
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112 test-data/k12_edited_proteins.fasta
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113 test-data/k12_ten_proteins.fasta
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114 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
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115 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular
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116 test-data/rbh_blastp_k12.tabular
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117 test-data/rbh_blastp_k12_self.tabular
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118 test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular
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119 test-data/rbh_none.tabular
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120 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular
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121 test-data/rhodopsin_nucs.fasta
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122 test-data/rhodopsin_proteins.fasta
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123 test-data/three_human_mRNA.fasta
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124 tools/blast_rbh/README.rst
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125 tools/blast_rbh/blast_rbh.py
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126 tools/blast_rbh/blast_rbh.xml
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127 tools/blast_rbh/tool_dependencies.xml
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129
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130 Licence (MIT)
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131 =============
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132
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133 Permission is hereby granted, free of charge, to any person obtaining a copy
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134 of this software and associated documentation files (the "Software"), to deal
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135 in the Software without restriction, including without limitation the rights
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136 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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137 copies of the Software, and to permit persons to whom the Software is
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138 furnished to do so, subject to the following conditions:
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139
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140 The above copyright notice and this permission notice shall be included in
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141 all copies or substantial portions of the Software.
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142
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143 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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144 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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145 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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146 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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147 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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148 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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149 THE SOFTWARE.