Repository revision
repository tip
Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository 'clinod'
http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
hg clone http://toolshed.g2.bx.psu.edu/repos/peterjc/clinod
clinod
unrestricted
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
3:6a9debe4b860
peterjc
True
245

Repository README files - may contain important installation or license information

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)
  • README.rst (this 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. Then:

$ ./run_functional_tests.sh -id clinod

That's it.

History

Version Changes
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.
v0.0.6
  • Adopted standard MIT licence.
  • Use reStructuredText for this README file.
  • Updated citation information (Cock et al. 2013).
  • Development moved to GitHub, https://github.com/peterjc/pico_galaxy

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/clinod

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/README.rst tools/clinod/clinod.xml 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/README.rst
tools/clinod/clinod.xml
tools/clinod/tool_dependencies.xml
test-data/four_human_proteins.fasta
test-data/four_human_proteins.clinod-1.3.tabular

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. Command line NoD is available and licenced separately.

Dependencies of this repository

Name Version Type
clinod 1.3 package

Contents of this repository

Name Description Version
Nucleolar localization sequence Detector (NoD) Find nucleolar localization signals (NoLSs) in protein sequences 0.0.5

Automated tool test results

Time tested: 2014-04-23 07:36:19
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13181:7a7985a007fb
Galaxy database version: 118
Tool shed revision: 13123:e6876f691854
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: clinod
Tool version: clinod
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/clinod/clinod/0.0.5)
TypeNameVersion
clinod package 1.3
Installation directory
/ToolDepsMain/clinod/1.3/peterjc/clinod/6a9debe4b860
Time tested: 2014-04-17 05:40:12
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13085:c05752549163
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: clinod
Tool version: clinod
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/clinod/clinod/0.0.5)
TypeNameVersion
clinod package 1.3
Installation directory
/ToolDepsMain/clinod/1.3/peterjc/clinod/6a9debe4b860
Time tested: 2014-04-16 05:34:34
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13065:1ad62c772728
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: clinod
Tool version: clinod
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/clinod/clinod/0.0.5)
TypeNameVersion
clinod package 1.3
Installation directory
/ToolDepsMain/clinod/1.3/peterjc/clinod/6a9debe4b860
Time tested: 2014-04-15 06:08:59
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13058:1165a5a1221a
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: clinod
Tool version: clinod
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/clinod/clinod/0.0.5)
TypeNameVersion
clinod package 1.3
Installation directory
/ToolDepsMain/clinod/1.3/peterjc/clinod/6a9debe4b860

Categories
Sequence Analysis