Mercurial > repos > peterjc > blast_rbh
annotate tools/blast_rbh/README.rst @ 6:e47960bcdccb draft
Uploaded v0.1.0f, exclude tied best hits
| author | peterjc |
|---|---|
| date | Wed, 21 May 2014 06:33:50 -0400 |
| parents | c84b6c21e3d4 |
| children | d3eb5cda7270 |
| rev | line source |
|---|---|
| 0 | 1 Galaxy tool to find BLAST Reciprocal Best Hits (RBH) |
| 2 ==================================================== | |
| 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 | |
| 9 pair of sequence files, and extract the reciprocal best hits. | |
| 10 | |
| 11 This is a work in progress, and builds on an earlier implementation which | |
| 12 prequired the two BLAST searches be prepared in advance. Integration allows | |
| 13 a much simpler user experience, and can ensure sensible filters are used. | |
| 14 | |
| 15 | |
| 16 Automated Installation | |
| 17 ====================== | |
| 18 | |
| 19 Installation via the Galaxy Tool Shed should take care of the Galaxy side of | |
| 20 things, including the dependency the NCBI BLAST+ binaries. | |
| 21 | |
| 22 | |
| 23 Manual Installation | |
| 24 =================== | |
| 25 | |
| 26 There are just two files to install: | |
| 27 | |
| 28 - ``blast_rbh.py`` (the Python script) | |
| 29 - ``blast_rbh.xml`` (the Galaxy tool definition) | |
| 30 | |
| 31 The suggested location is in a ``tools/blast_rbh/`` folder. You will then | |
| 32 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool | |
| 33 by adding the line:: | |
| 34 | |
| 35 <tool file="blast_rbh/blast_rbh.xml" /> | |
| 36 | |
| 37 If you want to run the functional tests, include the same line in your | |
| 38 ``tool_conf.xml.sample`` file, and the sample test files under Galaxy's | |
| 39 ``test-data/`` directory. Then:: | |
| 40 | |
| 41 ./run_functional_tests.sh -id blast_reciprocal_best_hits | |
| 42 | |
| 43 You will need to have the NCBI BLAST+ binaries installed and on the ``$PATH``. | |
| 44 | |
| 45 | |
| 46 History | |
| 47 ======= | |
| 48 | |
| 49 ======= ====================================================================== | |
| 50 Version Changes | |
| 51 ------- ---------------------------------------------------------------------- | |
| 52 v0.1.0 - Initial public release, targetting NCBI BLAST+ 2.2.29 | |
| 53 ======= ====================================================================== | |
| 54 | |
| 55 | |
| 56 Developers | |
| 57 ========== | |
| 58 | |
| 59 This tool is developed on the following GitHub repository: | |
| 60 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | |
| 61 | |
| 62 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
| 63 the following command from the Galaxy root folder:: | |
| 64 | |
| 6 | 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/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 |
| 0 | 66 |
| 67 Check this worked:: | |
| 68 | |
| 69 $ tar -tzf blast_rbh.tar.gz | |
| 70 tools/blast_rbh/README.rst | |
| 71 tools/blast_rbh/blast_rbh.xml | |
| 72 tools/blast_rbh/blast_rbh.py | |
| 73 tools/blast_rbh/repository_dependencies.xml | |
| 74 test-data/rhodopsin_nucs.fasta | |
| 1 | 75 test-data/rhodopsin_proteins.fasta |
| 0 | 76 test-data/three_human_mRNA.fasta |
| 1 | 77 test-data/four_human_proteins.fasta |
| 6 | 78 test-data/k12_edited_proteins.fasta |
| 79 test-data/k12_ten_proteins.fasta | |
| 0 | 80 test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular |
| 81 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular | |
| 1 | 82 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular |
| 0 | 83 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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|
84 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular |
| 6 | 85 test-data/rbh_blastp_k12.tabular |
| 0 | 86 |
| 87 | |
| 88 Licence (MIT) | |
| 89 ============= | |
| 90 | |
| 91 Permission is hereby granted, free of charge, to any person obtaining a copy | |
| 92 of this software and associated documentation files (the "Software"), to deal | |
| 93 in the Software without restriction, including without limitation the rights | |
| 94 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| 95 copies of the Software, and to permit persons to whom the Software is | |
| 96 furnished to do so, subject to the following conditions: | |
| 97 | |
| 98 The above copyright notice and this permission notice shall be included in | |
| 99 all copies or substantial portions of the Software. | |
| 100 | |
| 101 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 102 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 103 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| 104 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 105 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 106 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| 107 THE SOFTWARE. |