Mercurial > repos > bjoern-gruening > antismash
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author | bjoern-gruening |
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date | Thu, 15 Mar 2012 05:23:03 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.txt Thu Mar 15 05:23:03 2012 -0400 @@ -0,0 +1,71 @@ +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. +