Mercurial > repos > peterjc > blast_rbh

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v0.3.0 - Updated to BLAST+ 2.9.0 via conda; removed legacy tool packages.
author peterjc
date Wed, 07 Dec 2022 09:58:43 +0000
parents 38fe3aaa15aa
children
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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 2011-2017 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. 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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18
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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:
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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 *GigaScience* 2015, 4:39
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27 https://doi.org/10.1186/s13742-015-0080-7
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29 You should also cite the NCBI BLAST+ tools:
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30
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31 BLAST+: architecture and applications.
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32 C. Camacho et al. *BMC Bioinformatics* 2009, 10:421.
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33 https://doi.org/10.1186/1471-2105-10-421
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35
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36 Automated Installation
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37 ======================
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38
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39 Installation via the Galaxy Tool Shed should take care of the Galaxy side of
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40 things, including the dependency the NCBI BLAST+ binaries.
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42
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43 Manual Installation
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44 ===================
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45
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46 There are just three files to install:
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47
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48 - ``blast_rbh.py`` (the Python script)
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49 - ``best_hits.py`` (helper script, put in same directory)
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50 - ``blast_rbh.xml`` (the Galaxy tool definition)
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51
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52 The suggested location is in a ``tools/blast_rbh/`` folder. You will then
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53 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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54 by adding the line::
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55
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56 <tool file="blast_rbh/blast_rbh.xml" />
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57
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58 If you want to run the functional tests, copy the sample test files under
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59 sample test files under Galaxy's ``test-data/`` directory. Then::
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60
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61 ./run_tests.sh -id blast_reciprocal_best_hits
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63 You will need to have the NCBI BLAST+ binaries installed and on the ``$PATH``.
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66 History
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67 =======
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68
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69 ======= ======================================================================
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70 Version Changes
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71 ------- ----------------------------------------------------------------------
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72 v0.1.0 - Initial Test Tool Shed release, targetting NCBI BLAST+ 2.2.29
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73 v0.1.1 - Supports self-comparison, sometimes useful for spotting duplicates.
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74 v0.1.2 - Using optparse for command line API.
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75 - Tool definition now embeds citation information.
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76 - Fixed Tool Shed dependency definition.
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77 v0.1.3 - Option to make FASTA files non-redundant (via Biopython dependency).
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78 - Avoid extra database and BLAST search in self-comparison mode.
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79 v0.1.4 - Check for duplicate FASTA identifiers (workaround for makeblastdb
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80 not treating this as an error, leading to confusing RBH output).
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81 v0.1.5 - Clarify documentation for using the Python script outside Galaxy.
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82 - Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install.
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83 v0.1.6 - Offer the new blastp-fast task added in BLAST+ 2.2.30.
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84 - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
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85 v0.1.7 - Reorder XML elements (internal change only).
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86 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
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87 - Updated citation information with GigaScience paper.
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88 v0.1.8 - Updated to depend on NCBI BLAST+ 2.2.31 via ToolShed install.
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89 v0.1.9 - Updates to the command line API for the Python script.
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90 - PEP8 style updates to the Python script (internal change only).
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91 - Fix parameter help text which was not being displayed.
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92 v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda.
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93 - Update Biopython dependency.
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94 - Tweak Python script to work under Python 2 or Python 3.
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95 v0.1.12 - Use ``<command detect_errors="aggressive">`` (internal change only).
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96 - Single quote command line arguments (internal change only).
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97 v0.2.0 - Refactored to use more than one Python file (internal change only).
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98 v0.3.0 - Updated to BLAST+ 2.9.0 via conda; removed legacy tool packages.
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99 ======= ======================================================================
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101
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102 Developers
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103 ==========
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104
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105 This tool is developed on the following GitHub repository:
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106 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
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107
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108 For pushing a release to the test or main "Galaxy Tool Shed", use the following
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109 Planemo commands (which requires you have set your Tool Shed access details in
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110 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
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111
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112 $ planemo shed_update -t testtoolshed --check_diff tools/blast_rbh/
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113 ...
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115 or::
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116
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117 $ planemo shed_update -t toolshed --check_diff tools/blast_rbh/
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118 ...
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120 To just build and check the tar ball, use::
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121
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122 $ planemo shed_upload --tar_only tools/blast_rbh/
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123 ...
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124 $ tar -tzf shed_upload.tar.gz
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125 test-data/four_human_proteins.fasta
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126 test-data/k12_edited_proteins.fasta
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127 test-data/k12_ten_proteins.fasta
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128 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
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129 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular
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130 test-data/rbh_blastp_k12.tabular
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131 test-data/rbh_blastp_k12_self.tabular
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132 test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular
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133 test-data/rbh_none.tabular
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134 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular
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135 test-data/rhodopsin_nucs.fasta
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136 test-data/rhodopsin_proteins.fasta
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137 test-data/three_human_mRNA.fasta
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138 tools/blast_rbh/README.rst
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139 tools/blast_rbh/blast_rbh.py
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140 tools/blast_rbh/blast_rbh.xml
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141 tools/blast_rbh/tool_dependencies.xml
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142
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143
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144 Licence (MIT)
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145 =============
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146
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147 Permission is hereby granted, free of charge, to any person obtaining a copy
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148 of this software and associated documentation files (the "Software"), to deal
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149 in the Software without restriction, including without limitation the rights
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150 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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151 copies of the Software, and to permit persons to whom the Software is
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152 furnished to do so, subject to the following conditions:
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153
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154 The above copyright notice and this permission notice shall be included in
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155 all copies or substantial portions of the Software.
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156
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157 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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158 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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159 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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160 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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161 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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162 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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163 THE SOFTWARE.