Galaxy wrapper for EffectiveT3 v1.0.1

This wrapper is copyright 2011-2017 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. https://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. https://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 its associated models (animal, plant and standard).

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)
• README.rst (this 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 move/copy the test-data/ files under Galaxy's test-data/ folder. Then:

$ ./run_tests.sh -id effectiveT3

That's it.

History

Developers

This script and related tools were initially developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools

Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3

For pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ~/.planemo.yml and that you have access rights on the Tool Shed):

$ planemo shed_update -t testtoolshed --check_diff tools/effectiveT3/
...

or:

$ planemo shed_update -t toolshed --check_diff tools/effectiveT3/
...

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only tools/effectiveT3/
...
$ tar -tzf shed_upload.tar.gz
tool-data/effectiveT3.loc.sample
test-data/empty.fasta
test-data/empty_effectiveT3.tabular
test-data/four_human_proteins.fasta
test-data/four_human_proteins.effectiveT3.tabular
tool-data/effectiveT3.loc.sample
tools/effectiveT3/README.rst
tools/effectiveT3/effectiveT3.py
tools/effectiveT3/effectiveT3.xml
tools/effectiveT3/tool_dependencies.xml

Licence (MIT)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

NOTE: This is the licence for the Galaxy Wrapper only. EffectiveT3 is available and licenced separately.