Mercurial > repos > peterjc > blast_rbh
annotate tools/blast_rbh/README.rst @ 12:661276ad882e draft
Uploaded v0.1.3, uses Biopython for making NR
| author | peterjc |
|---|---|
| date | Tue, 14 Oct 2014 06:53:40 -0400 |
| parents | 4733e4ea4dab |
| children | 4454596ed127 |
| 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 | |
| 12 | 11 It is available from the Galaxy Tool Shed at: |
| 12 http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh | |
| 0 | 13 |
| 14 | |
| 15 Automated Installation | |
| 16 ====================== | |
| 17 | |
| 18 Installation via the Galaxy Tool Shed should take care of the Galaxy side of | |
| 19 things, including the dependency the NCBI BLAST+ binaries. | |
| 20 | |
| 21 | |
| 22 Manual Installation | |
| 23 =================== | |
| 24 | |
| 25 There are just two files to install: | |
| 26 | |
| 27 - ``blast_rbh.py`` (the Python script) | |
| 28 - ``blast_rbh.xml`` (the Galaxy tool definition) | |
| 29 | |
| 30 The suggested location is in a ``tools/blast_rbh/`` folder. You will then | |
| 31 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool | |
| 32 by adding the line:: | |
| 33 | |
| 34 <tool file="blast_rbh/blast_rbh.xml" /> | |
| 35 | |
| 36 If you want to run the functional tests, include the same line in your | |
| 37 ``tool_conf.xml.sample`` file, and the sample test files under Galaxy's | |
| 38 ``test-data/`` directory. Then:: | |
| 39 | |
| 40 ./run_functional_tests.sh -id blast_reciprocal_best_hits | |
| 41 | |
| 42 You will need to have the NCBI BLAST+ binaries installed and on the ``$PATH``. | |
| 43 | |
| 44 | |
| 45 History | |
| 46 ======= | |
| 47 | |
| 48 ======= ====================================================================== | |
| 49 Version Changes | |
| 50 ------- ---------------------------------------------------------------------- | |
| 10 | 51 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
peterjc
parents:
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changeset
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52 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
parents:
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changeset
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53 v0.1.2 - Using optparse for command line API. |
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11
4733e4ea4dab
Uploaded v0.1.2c, same defaults in blast_rbh.py as blast_rbh.xml
peterjc
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54 - Tool definition now embeds citation information. |
| 10 | 55 - Fixed Tool Shed dependency definition. |
| 12 | 56 v0.1.3 - Option to make FASTA files non-redundant (via Biopython dependency). |
| 57 - Avoid extra database and BLAST search in self-comparison mode. | |
| 0 | 58 ======= ====================================================================== |
| 59 | |
| 60 | |
| 61 Developers | |
| 62 ========== | |
| 63 | |
| 64 This tool is developed on the following GitHub repository: | |
| 65 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | |
| 66 | |
| 67 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
| 68 the following command from the Galaxy root folder:: | |
| 69 | |
| 10 | 70 $ 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 | 71 |
| 72 Check this worked:: | |
| 73 | |
| 74 $ tar -tzf blast_rbh.tar.gz | |
| 75 tools/blast_rbh/README.rst | |
| 76 tools/blast_rbh/blast_rbh.xml | |
| 77 tools/blast_rbh/blast_rbh.py | |
| 10 | 78 tools/blast_rbh/tool_dependencies.xml |
| 0 | 79 test-data/rhodopsin_nucs.fasta |
| 1 | 80 test-data/rhodopsin_proteins.fasta |
| 0 | 81 test-data/three_human_mRNA.fasta |
| 1 | 82 test-data/four_human_proteins.fasta |
| 6 | 83 test-data/k12_edited_proteins.fasta |
| 84 test-data/k12_ten_proteins.fasta | |
| 0 | 85 test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular |
| 86 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular | |
| 1 | 87 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular |
| 0 | 88 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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89 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular |
| 6 | 90 test-data/rbh_blastp_k12.tabular |
| 9 | 91 test-data/rbh_blastp_k12_self.tabular |
| 0 | 92 |
| 93 | |
| 94 Licence (MIT) | |
| 95 ============= | |
| 96 | |
| 97 Permission is hereby granted, free of charge, to any person obtaining a copy | |
| 98 of this software and associated documentation files (the "Software"), to deal | |
| 99 in the Software without restriction, including without limitation the rights | |
| 100 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| 101 copies of the Software, and to permit persons to whom the Software is | |
| 102 furnished to do so, subject to the following conditions: | |
| 103 | |
| 104 The above copyright notice and this permission notice shall be included in | |
| 105 all copies or substantial portions of the Software. | |
| 106 | |
| 107 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 108 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 109 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| 110 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 111 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 112 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| 113 THE SOFTWARE. |