Mercurial > repos > peterjc > effectivet3
view tools/protein_analysis/effectiveT3.txt @ 0:43436379876f
Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
author | peterjc |
---|---|
date | Tue, 07 Jun 2011 17:21:30 -0400 |
parents | |
children | e607c342312f |
line wrap: on
line source
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/ 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) 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 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 Check this worked: $ tar -tzf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt 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. NLStradamus is available and licenced separately.