Mercurial > repos > bgruening > antismash
diff readme.rst @ 0:5db064bbb3be draft
Imported from capsule None
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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Tue Jul 15 14:34:55 2014 -0400 @@ -0,0 +1,65 @@ +Galaxy wrapper for AntiSmash +===================================== + +This wrapper is copyright 2012-2014 by Björn Grüning. + +This is a wrapper for the command line tool of antiSMASH. + +antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. +It integrates and cross-links with a large number of in silico secondary metabolite analysis tools. + +http://antismash.secondarymetabolites.org/ + +Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano (2011). +antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346. + + +Installation +============ + +Galaxy should be able to automatically install the dependencies, i.e. the +'package_hmmer_3_0' or 'package_blast_plus_2_2_28' repository. + +You must tell Galaxy about any system level Pfam databases using the configuration +file antismash.loc. + +You can download the Pfam provided databases as compressed archives from here: + +* ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/ + + +External Data +============= + +The antismash.loc file contains the path to a Pfam database. +For any other tool that also uses a Pfam database *.log file, you can sync or link both *.loc files. + + + +History +======= + +v0.1 - Initial public release + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. +