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author bgruening
date Tue, 15 Jul 2014 14:34:55 -0400
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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