Mercurial > repos > peterjc > blast_rbh
annotate tools/blast_rbh/README.rst @ 13:4454596ed127 draft
Uploaded
| author | peterjc |
|---|---|
| date | Thu, 30 Oct 2014 14:20:48 -0400 |
| parents | 661276ad882e |
| children | 40c85a67e645 |
| rev | line source |
|---|---|
| 13 | 1 Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper |
| 2 ========================================================== | |
| 0 | 3 |
| 4 This tool is copyright 2011-2014 by Peter Cock, The James Hutton Institute | |
| 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
| 6 See the licence text below. | |
| 7 | |
| 8 This tool is a short Python script to run reciprocal BLAST searches on a | |
| 13 | 9 pair of sequence files, and extract the reciprocal best hits. The script |
| 10 ``blast_rbh.py`` can be used directly (without Galaxy) as long as NCBI | |
| 11 BLAST+ is installed. | |
| 0 | 12 |
| 13 | 13 It comes with an optional Galaxy tool definition file ``blast_rbh.xml`` |
| 14 allowing the Python script to be run from within Galaxy. It is available | |
| 15 from the Galaxy Tool Shed at: | |
| 12 | 16 http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh |
| 0 | 17 |
| 18 | |
| 19 Automated Installation | |
| 20 ====================== | |
| 21 | |
| 22 Installation via the Galaxy Tool Shed should take care of the Galaxy side of | |
| 23 things, including the dependency the NCBI BLAST+ binaries. | |
| 24 | |
| 25 | |
| 26 Manual Installation | |
| 27 =================== | |
| 28 | |
| 29 There are just two files to install: | |
| 30 | |
| 31 - ``blast_rbh.py`` (the Python script) | |
| 32 - ``blast_rbh.xml`` (the Galaxy tool definition) | |
| 33 | |
| 34 The suggested location is in a ``tools/blast_rbh/`` folder. You will then | |
| 35 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool | |
| 36 by adding the line:: | |
| 37 | |
| 38 <tool file="blast_rbh/blast_rbh.xml" /> | |
| 39 | |
| 13 | 40 If you want to run the functional tests, copy the sample test files under |
| 41 sample test files under Galaxy's ``test-data/`` directory. Then:: | |
| 0 | 42 |
| 13 | 43 ./run_tests.sh -id blast_reciprocal_best_hits |
| 0 | 44 |
| 45 You will need to have the NCBI BLAST+ binaries installed and on the ``$PATH``. | |
| 46 | |
| 47 | |
| 48 History | |
| 49 ======= | |
| 50 | |
| 51 ======= ====================================================================== | |
| 52 Version Changes | |
| 53 ------- ---------------------------------------------------------------------- | |
| 10 | 54 v0.1.0 - Initial Test Tool Shed release, targetting NCBI BLAST+ 2.2.29 |
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d3eb5cda7270
Uploaded v0.1.2, self comparison and easier command line API
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55 v0.1.1 - Supports self-comparison, sometimes useful for spotting duplicates. |
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d3eb5cda7270
Uploaded v0.1.2, self comparison and easier command line API
peterjc
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56 v0.1.2 - Using optparse for command line API. |
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4733e4ea4dab
Uploaded v0.1.2c, same defaults in blast_rbh.py as blast_rbh.xml
peterjc
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57 - Tool definition now embeds citation information. |
| 10 | 58 - Fixed Tool Shed dependency definition. |
| 12 | 59 v0.1.3 - Option to make FASTA files non-redundant (via Biopython dependency). |
| 60 - Avoid extra database and BLAST search in self-comparison mode. | |
| 13 | 61 v0.1.4 - Check for duplicate FASTA identifiers (workaround for makeblastdb |
| 62 not treating this as an error, leading to confusing RBH output). | |
| 63 v0.1.5 - Clarify documentation for using the Python script outside Galaxy. | |
| 64 - Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install. | |
| 0 | 65 ======= ====================================================================== |
| 66 | |
| 67 | |
| 68 Developers | |
| 69 ========== | |
| 70 | |
| 71 This tool is developed on the following GitHub repository: | |
| 72 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | |
| 73 | |
| 74 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
| 75 the following command from the Galaxy root folder:: | |
| 76 | |
| 10 | 77 $ 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/tool_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/k12_edited_proteins.fasta test-data/k12_ten_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 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastp_k12.tabular test-data/rbh_blastp_k12_self.tabular |
| 0 | 78 |
| 79 Check this worked:: | |
| 80 | |
| 81 $ tar -tzf blast_rbh.tar.gz | |
| 82 tools/blast_rbh/README.rst | |
| 83 tools/blast_rbh/blast_rbh.xml | |
| 84 tools/blast_rbh/blast_rbh.py | |
| 10 | 85 tools/blast_rbh/tool_dependencies.xml |
| 0 | 86 test-data/rhodopsin_nucs.fasta |
| 1 | 87 test-data/rhodopsin_proteins.fasta |
| 0 | 88 test-data/three_human_mRNA.fasta |
| 1 | 89 test-data/four_human_proteins.fasta |
| 6 | 90 test-data/k12_edited_proteins.fasta |
| 91 test-data/k12_ten_proteins.fasta | |
| 0 | 92 test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular |
| 93 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular | |
| 1 | 94 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular |
| 0 | 95 test-data/rbh_none.tabular |
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c84b6c21e3d4
Uploaded v0.1.0e, test TBLASTX mode; more columns in output
peterjc
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96 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular |
| 6 | 97 test-data/rbh_blastp_k12.tabular |
| 9 | 98 test-data/rbh_blastp_k12_self.tabular |
| 0 | 99 |
| 100 | |
| 101 Licence (MIT) | |
| 102 ============= | |
| 103 | |
| 104 Permission is hereby granted, free of charge, to any person obtaining a copy | |
| 105 of this software and associated documentation files (the "Software"), to deal | |
| 106 in the Software without restriction, including without limitation the rights | |
| 107 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| 108 copies of the Software, and to permit persons to whom the Software is | |
| 109 furnished to do so, subject to the following conditions: | |
| 110 | |
| 111 The above copyright notice and this permission notice shall be included in | |
| 112 all copies or substantial portions of the Software. | |
| 113 | |
| 114 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 115 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 116 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| 117 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 118 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 119 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| 120 THE SOFTWARE. |