view tools/protein_analysis/clinod.txt @ 1:221d7dca03a5 draft

Uploaded v0.0.4, which adds a unit test

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

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.

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/


Installation
============
This wrapper expects the java binary to be on the system PATH, and to be able
to access command line NoD as /opt/clinod/clinod-1.3.jar (edit clinod.xml if
you wish to use a different location).

Internally NoD calls the binary batchman from the Stuttgart Neural Network
Simulator (SNNS) v 4.2 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/protein_analysis 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="protein_analysis/clinod.xml" />

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


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/protein_analysis/clinod.xml tools/protein_analysis/clinod.txt test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular

Check this worked:

$ tar -tzf clinod.tar.gz
tools/protein_analysis/clinod.xml
tools/protein_analysis/clinod.txt
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.