Mercurial > repos > peterjc > blast_rbh
annotate tools/blast_rbh/README.rst @ 10:982458013bdb draft
Uploaded v0.1.2b, fixed dependency definition
author | peterjc |
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date | Thu, 31 Jul 2014 05:01:51 -0400 |
parents | 95190ebd4657 |
children | 4733e4ea4dab |
rev | line source |
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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 ------- ---------------------------------------------------------------------- | |
10 | 52 v0.1.0 - Initial Test Tool Shed release, targetting NCBI BLAST+ 2.2.29 |
8
d3eb5cda7270
Uploaded v0.1.2, self comparison and easier command line API
peterjc
parents:
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changeset
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53 v0.1.1 - Supports self-comparison, sometimes useful for spotting duplicates. |
d3eb5cda7270
Uploaded v0.1.2, self comparison and easier command line API
peterjc
parents:
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changeset
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54 v0.1.2 - Using optparse for command line API. |
10 | 55 - Fixed Tool Shed dependency definition. |
0 | 56 ======= ====================================================================== |
57 | |
58 | |
59 Developers | |
60 ========== | |
61 | |
62 This tool is developed on the following GitHub repository: | |
63 https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh | |
64 | |
65 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
66 the following command from the Galaxy root folder:: | |
67 | |
10 | 68 $ 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 | 69 |
70 Check this worked:: | |
71 | |
72 $ tar -tzf blast_rbh.tar.gz | |
73 tools/blast_rbh/README.rst | |
74 tools/blast_rbh/blast_rbh.xml | |
75 tools/blast_rbh/blast_rbh.py | |
10 | 76 tools/blast_rbh/tool_dependencies.xml |
0 | 77 test-data/rhodopsin_nucs.fasta |
1 | 78 test-data/rhodopsin_proteins.fasta |
0 | 79 test-data/three_human_mRNA.fasta |
1 | 80 test-data/four_human_proteins.fasta |
6 | 81 test-data/k12_edited_proteins.fasta |
82 test-data/k12_ten_proteins.fasta | |
0 | 83 test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular |
84 test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular | |
1 | 85 test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular |
0 | 86 test-data/rbh_none.tabular |
5
c84b6c21e3d4
Uploaded v0.1.0e, test TBLASTX mode; more columns in output
peterjc
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87 test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular |
6 | 88 test-data/rbh_blastp_k12.tabular |
9 | 89 test-data/rbh_blastp_k12_self.tabular |
0 | 90 |
91 | |
92 Licence (MIT) | |
93 ============= | |
94 | |
95 Permission is hereby granted, free of charge, to any person obtaining a copy | |
96 of this software and associated documentation files (the "Software"), to deal | |
97 in the Software without restriction, including without limitation the rights | |
98 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
99 copies of the Software, and to permit persons to whom the Software is | |
100 furnished to do so, subject to the following conditions: | |
101 | |
102 The above copyright notice and this permission notice shall be included in | |
103 all copies or substantial portions of the Software. | |
104 | |
105 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
106 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
107 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
108 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
109 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
110 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
111 THE SOFTWARE. |