# HG changeset patch
# User bgruening
# Date 1380871985 14400
# Node ID 7ad005dfbe78570538b76d0b19512aade5ca4afb
Uploaded
diff -r 000000000000 -r 7ad005dfbe78 antismash.xml
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+++ b/antismash.xml Fri Oct 04 03:33:05 2013 -0400
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+
+ and Antibiotics Analysis (antiSMASH)
+ run_antismash.py
+
+ --input $infile
+ --cpus 4
+ #set $type_list = ','.join([$type for $type in $types])
+ --enable $type_list
+ --input-type nucl
+ $smcogs
+ $clusterblast
+ $subclusterblast
+ $inclusive
+ $full_hmmer
+ $full_blast
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+ ##--from START Start analysis at nucleotide specified
+ ##--to END
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+ (wg_blast == True or pfam == True)
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+.. class:: infomark
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+That version of antiSMASH can only handle one sequence. So multi-sequence FASTA files are not supported.
+For multiple sequences please use multi-antiSMASH. The advantage of that tool is that it will provide you with a
+archive of all results created from antiSMASH (It can be large!) and a HTML output, for better inspection.
+
+
+**What it does**
+
+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 that have been published earlier.
+
+
+**Input**
+
+If you don't have an annotated GenBank or embl file you also can provide a glimmer prediction output. You can created it with glimmer or glimmerHMM.
+
+
+**References**
+
+Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber,
+Rainer Breitling and Eriko Takano (2011). antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research, doi: 10.1093/nar/gkr466.
+
+http://antismash.secondarymetabolites.org/help.html
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diff -r 000000000000 -r 7ad005dfbe78 readme.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.txt Fri Oct 04 03:33:05 2013 -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:
+
+
+https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2
+
+
+... 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:
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+
+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.
+
diff -r 000000000000 -r 7ad005dfbe78 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Oct 04 03:33:05 2013 -0400
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+ https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip
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+ .
+ $INSTALL_DIR
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+ $INSTALL_DIR/run_antismash.py
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+ https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2
+
+ .
+ $INSTALL_DIR
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+ $INSTALL_DIR/run_antismash.py
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+ https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.i686.tar.bz2
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+ .
+ $INSTALL_DIR
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+ $INSTALL_DIR/run_antismash.py
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+ biopython=1.62
+helperlibs=0.1.2
+straight.plugin=1.4.0-post-1
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+ $INSTALL_DIR
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+ AntiSmash installation with all dependencies.
+
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+