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author bjoern-gruening
date Thu, 15 Mar 2012 05:23:03 -0400
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+Galaxy wrapper for AntiSmash
+=====================================
+
+This wrapper is copyright 2012 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
+============
+
+Currently these wrapper is tested with version 1.1 and the modified version of antismash.py included in that repository.
+
+Install or downlaod antiSMASH from:
+
+http://antismash.secondarymetabolites.org/download.html
+
+... and follow the instructions.
+Please replace the antismash.py file with the one inlcuded in that repository.
+Edit the following lines in multi_antiSMASH_wrapper.py and antiSMASH_wrapper.py and adopt it to your installation.
+
+blastdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
+pfamdbpath = '/home/galaxy/bin/antismash-1.1.0/db'
+antismash_path = '/home/galaxy/bin/antismash-1.1.0/antismash.py'
+
+
+To install the wrapper copy the antiSMASH folder in the galaxy tools
+folder and modify the tools_conf.xml file to make the tool available to Galaxy.
+For example:
+
+<section name="PKS-NRPS prediction" id="pks-nrps_prediction">
+    <tool file="pks-nrps/tools/antiSMASH/antiSMASH.xml" />
+    <tool file="pks-nrps/tools/antiSMASH/multi_antiSMASH.xml" />
+</section>
+
+
+History
+=======
+
+v0.1 - Initial public release
+
+
+Wrapper Licence (MIT/BSD style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+