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Repository 'clinod'
http://toolshed.g2.bx.psu.edu/view/peterjc/clinod/b8be455c27d1
hg clone http://toolshed.g2.bx.psu.edu/repos/peterjc/clinod
clinod
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NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins
NoD is a predictor of nucleolar localization sequences (NoLSs) in proteins. NoLSs are short basic motifs that localize proteins to the nucleolus, a sub-compartment of the nucleus.
http://www.compbio.dundee.ac.uk/www-nod/

This is a Galaxy wrapper for command line nod (clinod) v1.3
0:b8be455c27d1
peterjc
True
242

Repository README files - may contain important installation or license information

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: That's it. History ======= v0.0.1 - 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 clinod.tar.gz tools/protein_analysis/clinod.xml tools/protein_analysis/clinod.txt Check this worked: $ tar -tzf clinod.tar.gz tools/protein_analysis/clinod.xml tools/protein_analysis/clinod.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. Command line NoD is available and licenced separately.

Contents of this repository

Name Description Version
Nucleolar localization sequence Detector (NoD) Find nucleolar localization signals (NoLSs) in protein sequences 0.0.1

Automated tool test results

Time tested: 2014-02-13 12:54:28
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 12484:b463c73f3348
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: clinod
Tool version: 0.0.1
Tool guid: toolshed.g2.bx.psu.edu/repos/peterjc/clinod/clinod/0.0.1
Missing components:
Repository does not have a test-data directory. Functional test definitions missing for clinod.

Categories
Sequence Analysis