|
0
|
1 Galaxy wrapper for AntiSmash
|
|
|
2 =====================================
|
|
|
3
|
|
|
4 This wrapper is copyright 2012 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 Currently these wrapper is tested with version 1.1 and the modified version of antismash.py included in that repository.
|
|
|
21
|
|
|
22 Install or downlaod antiSMASH from:
|
|
|
23
|
|
|
24
|
|
|
25 https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2
|
|
|
26
|
|
|
27
|
|
|
28 ... and follow the instructions.
|
|
|
29 Please replace the antismash.py file with the one inlcuded in that repository.
|
|
|
30 Edit the following lines in multi_antiSMASH_wrapper.py and antiSMASH_wrapper.py and adopt it to your installation.
|
|
|
31
|
|
|
32 blastdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
|
|
|
33 pfamdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
|
|
|
34 antismash_path = '/home/galaxy/bin/antismash-1.1.0/antismash.py'
|
|
|
35
|
|
|
36
|
|
|
37 To install the wrapper copy the antiSMASH folder in the galaxy tools
|
|
|
38 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
|
|
|
39 For example:
|
|
|
40
|
|
|
41 <section name="PKS-NRPS prediction" id="pks-nrps_prediction">
|
|
|
42 <tool file="pks-nrps/tools/antiSMASH/antiSMASH.xml" />
|
|
|
43 <tool file="pks-nrps/tools/antiSMASH/multi_antiSMASH.xml" />
|
|
|
44 </section>
|
|
|
45
|
|
|
46
|
|
|
47 History
|
|
|
48 =======
|
|
|
49
|
|
|
50 v0.1 - Initial public release
|
|
|
51
|
|
|
52
|
|
|
53 Wrapper Licence (MIT/BSD style)
|
|
|
54 ===============================
|
|
|
55
|
|
|
56 Permission to use, copy, modify, and distribute this software and its
|
|
|
57 documentation with or without modifications and for any purpose and
|
|
|
58 without fee is hereby granted, provided that any copyright notices
|
|
|
59 appear in all copies and that both those copyright notices and this
|
|
|
60 permission notice appear in supporting documentation, and that the
|
|
|
61 names of the contributors or copyright holders not be used in
|
|
|
62 advertising or publicity pertaining to distribution of the software
|
|
|
63 without specific prior permission.
|
|
|
64
|
|
|
65 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
|
|
|
66 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
|
|
|
67 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
|
|
|
68 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
|
|
|
69 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
|
|
|
70 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
|
|
|
71 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
|
|
|
72 OR PERFORMANCE OF THIS SOFTWARE.
|
|
|
73
|
