diff readme.rst @ 0:5db064bbb3be draft

Imported from capsule None
author bgruening
date Tue, 15 Jul 2014 14:34:55 -0400
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+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.
+