Mercurial > repos > bgruening > antismash
comparison readme.rst @ 0:5db064bbb3be draft
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author | bgruening |
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date | Tue, 15 Jul 2014 14:34:55 -0400 |
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children | 593bb8f5488b |
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1 Galaxy wrapper for AntiSmash | |
2 ===================================== | |
3 | |
4 This wrapper is copyright 2012-2014 by Björn Grüning. | |
5 | |
6 This is a wrapper for the command line tool of antiSMASH. | |
7 | |
8 antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. | |
9 It integrates and cross-links with a large number of in silico secondary metabolite analysis tools. | |
10 | |
11 http://antismash.secondarymetabolites.org/ | |
12 | |
13 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano (2011). | |
14 antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346. | |
15 | |
16 | |
17 Installation | |
18 ============ | |
19 | |
20 Galaxy should be able to automatically install the dependencies, i.e. the | |
21 'package_hmmer_3_0' or 'package_blast_plus_2_2_28' repository. | |
22 | |
23 You must tell Galaxy about any system level Pfam databases using the configuration | |
24 file antismash.loc. | |
25 | |
26 You can download the Pfam provided databases as compressed archives from here: | |
27 | |
28 * ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/ | |
29 | |
30 | |
31 External Data | |
32 ============= | |
33 | |
34 The antismash.loc file contains the path to a Pfam database. | |
35 For any other tool that also uses a Pfam database *.log file, you can sync or link both *.loc files. | |
36 | |
37 | |
38 | |
39 History | |
40 ======= | |
41 | |
42 v0.1 - Initial public release | |
43 | |
44 | |
45 Licence (MIT) | |
46 ============= | |
47 | |
48 Permission is hereby granted, free of charge, to any person obtaining a copy | |
49 of this software and associated documentation files (the "Software"), to deal | |
50 in the Software without restriction, including without limitation the rights | |
51 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
52 copies of the Software, and to permit persons to whom the Software is | |
53 furnished to do so, subject to the following conditions: | |
54 | |
55 The above copyright notice and this permission notice shall be included in | |
56 all copies or substantial portions of the Software. | |
57 | |
58 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
59 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
60 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
61 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
62 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
63 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
64 THE SOFTWARE. | |
65 |