Mercurial > repos > bjoern-gruening > antismash
comparison readme.txt @ 0:6a37d0a4510a default tip
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| author | bjoern-gruening |
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| date | Thu, 15 Mar 2012 05:23:03 -0400 |
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| -1:000000000000 | 0:6a37d0a4510a |
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| 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 http://antismash.secondarymetabolites.org/download.html | |
| 25 | |
| 26 ... and follow the instructions. | |
| 27 Please replace the antismash.py file with the one inlcuded in that repository. | |
| 28 Edit the following lines in multi_antiSMASH_wrapper.py and antiSMASH_wrapper.py and adopt it to your installation. | |
| 29 | |
| 30 blastdbpath = '/home/galaxy/bin/antismash-1.1.0/db' | |
| 31 pfamdbpath = '/home/galaxy/bin/antismash-1.1.0/db' | |
| 32 antismash_path = '/home/galaxy/bin/antismash-1.1.0/antismash.py' | |
| 33 | |
| 34 | |
| 35 To install the wrapper copy the antiSMASH folder in the galaxy tools | |
| 36 folder and modify the tools_conf.xml file to make the tool available to Galaxy. | |
| 37 For example: | |
| 38 | |
| 39 <section name="PKS-NRPS prediction" id="pks-nrps_prediction"> | |
| 40 <tool file="pks-nrps/tools/antiSMASH/antiSMASH.xml" /> | |
| 41 <tool file="pks-nrps/tools/antiSMASH/multi_antiSMASH.xml" /> | |
| 42 </section> | |
| 43 | |
| 44 | |
| 45 History | |
| 46 ======= | |
| 47 | |
| 48 v0.1 - Initial public release | |
| 49 | |
| 50 | |
| 51 Wrapper Licence (MIT/BSD style) | |
| 52 =============================== | |
| 53 | |
| 54 Permission to use, copy, modify, and distribute this software and its | |
| 55 documentation with or without modifications and for any purpose and | |
| 56 without fee is hereby granted, provided that any copyright notices | |
| 57 appear in all copies and that both those copyright notices and this | |
| 58 permission notice appear in supporting documentation, and that the | |
| 59 names of the contributors or copyright holders not be used in | |
| 60 advertising or publicity pertaining to distribution of the software | |
| 61 without specific prior permission. | |
| 62 | |
| 63 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 64 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 65 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 66 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 67 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 68 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 69 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 70 OR PERFORMANCE OF THIS SOFTWARE. | |
| 71 |