Mercurial > repos > peterjc > effectivet3
view tools/protein_analysis/effectiveT3.txt @ 1:e607c342312f
Wrapper v0.0.8, includes effectiveT3.loc.sample file
author | peterjc |
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date | Tue, 02 Aug 2011 07:06:13 -0400 |
parents | 43436379876f |
children | 5a8e09f115f8 |
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Galaxy wrapper for EffectiveT3 v1.0.1 ===================================== This wrapper is copyright 2011 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. This is a wrapper for the command line Java tool EffectiveT3, v1.0.1, Jehl, Arnold and Rattei. Effective - a database of predicted secreted bacterial proteins Nucleic Acids Research, 39(Database issue), D591-5, 2011. http://dx.doi.org/10.1093/nar/gkq1154 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei. Sequence-based prediction of type III secreted proteins. PLoS Pathog. 5(4):e1000376, 2009. http://dx.doi.org/10.1371/journal.ppat.1000376 http://effectors.org/ Installation =========== You can change the path by editing the definition near the start of the Python script effectiveT3.py, but by default it expects the following files to be installed at these locations: /opt/EffectiveT3/TTSS_GUI-1.0.1.jar /opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar /opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar /opt/EffectiveT3/module/TTSS_STD-1.0.1.jar To install the wrapper copy or move the following files under the Galaxy tools folder, e.g. in a tools/protein_analysis folder: * effectiveT3.xml (the Galaxy tool definition) * effectiveT3.py (the Python wrapper script) * effectiveT3.txt (this README file) Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder (and edit if appropriate, e.g. to add or remove a model). You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. If you are using other protein analysis tools like TMHMM or SignalP, put it next to them. Just add the line: <tool file="protein_analysis/effectiveT3.xml" /> That's it. History ======= v0.0.7 - Initial public release v0.0.8 - Include effectiveT3.loc.sample in Tool Shed Developers ========== This script and related tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: $ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt tool-data/effectiveT3.loc.sample Check this worked: $ tar -tzf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt tool-data/effectiveT3.loc.sample 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. NOTE: This is the licence for the Galaxy Wrapper only. EffectiveT3 is available and licenced separately.