view tools/clinod/clinod.txt @ 2:d1aebb0acee7 draft

Uploaded v0.0.5, automated installation

Galaxy wrapper for Command line NoD predictor (v1.3)
====================================================

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.

Command line NoD predictor is a tool for predicting nucleolar localization
sequences (NoLSs) in a FASTA file of proteins using a neural network. There
is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/

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


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

This should be straightforward, Galaxy should automatically download and install
the JAR file for clinod v1.3 and the batchman executable from the Stuttgart
Neural Network Simulator (SNNS), and set the $CLINOD to their folder.


Manual Installation
===================
This wrapper expects the java binary to be on the system PATH, and to be able
to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used
/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod

Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network
Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the
system path or located next to the JAR file, i.e. /opt/clinod/batchman

To install the wrapper copy or move the following files under the Galaxy tools
folder, e.g. in a tools/clinod folder:

* clinod.xml (the Galaxy tool definition)
* clinod.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="clinod/clinod.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 clinod

That's it.


History
=======

v0.0.1 - Initial public release
v0.0.2 - Treat non-zero return codes as errors
v0.0.3 - Describe output table in help
v0.0.4 - Added unit test
v0.0.5 - Link to Tool Shed added to help text and this documentation.
       - Automated tool installation.


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 clinod.tar.gz tools/clinod/clinod.xml tools/clinod/clinod.txt tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular

Check this worked:

$ tar -tzf clinod.tar.gz
tools/clinod/clinod.xml
tools/clinod/clinod.txt
tools/clinod/tool_dependencies.xml
test-data/four_human_proteins.fasta
test-data/four_human_proteins.clinod-1.3.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. Command line
NoD is available and licenced separately.