view tools/effectiveT3/effectiveT3.txt @ 4:0c21abf1073b draft

Uploaded v0.0.11 take 3, adding links to Tool Shed entry

Galaxy wrapper for EffectiveT3 v1.0.1
=====================================

This wrapper is copyright 2011-2013 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/

This wrapper is available from the Galaxy Tool Shed at:
http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3


Automated Installation
======================

This should be straightforward, Galaxy should automatically download and install
the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std).


Manual Installation
===================

You can change the path by setting the environment variable EFFECTIVET3 to the
relevant folder, 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/effectiveT3 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="effectiveT3/effectiveT3.xml" />

If you wish to run the unit tests, also add this to tools_conf.xml.sample
and move/copy the test-data files under Galaxy's test-data folder.

$ ./run_functional_tests.sh -id effectiveT3

That's it.


History
=======

v0.0.7 - Initial public release
v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
v0.0.9 - Check the return code for errors in the XML
v0.0.10- Added unit test
v0.0.11- Automated installation
       - Record version of Python script when called from Galaxy
       - Link to Tool Shed added to help text and this documentation.


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://toolshed.g2.bx.psu.edu/ tarball use
the following command from the Galaxy root folder:

$ tar -czf effectiveT3.tar.gz tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.txt tools/effectiveT3/tool_dependencies.xml tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular


Check this worked:

$ tar -tzf effectiveT3.tar.gz
tools/effectiveT3/effectiveT3.xml
tools/effectiveT3/effectiveT3.py
tools/effectiveT3/effectiveT3.txt
tools/effectiveT3/tool_dependencies.xml
tool-data/effectiveT3.loc.sample
test-data/four_human_proteins.fasta
test-data/four_human_proteins.effectiveT3.tabular
test-data/empty.fasta
test-data/empty_effectiveT3.tabular


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.