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.shed.yml
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README.rst
README.rst
 
 
clinod.xml
clinod.xml
 
 
tool_dependencies.xml
tool_dependencies.xml
 
 

README.rst

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

This wrapper is copyright 2011-2015 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 availabe via a wapper script named clinod on the system $PATH.

Older versions of this tool called the JAR file directly via an environment variable as $CLINOD/clinod-1.3.jar - this is no longer used.

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 move/copy the test-data/ files under Galaxy's test-data/ folder. Then:

$ ./run_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
v0.0.7
  • Use the new $GALAXY_SLOTS environment variable for thread count.
  • Tool definition now embeds citation information.
v0.0.8
  • Reorder XML elements (internal change only).
  • Planemo for Tool Shed upload (.shed.yml, internal change only).
v0.0.9
  • Explicitly record clinod version via <version_command>.
v0.0.10
  • Use <command detect_errors="aggressive"> (internal change only).
  • Single quote command line arguments (internal change only).
v0.1.0
  • Calls the JAR file via a wrapper script clinod, in order to use the BioConda package OR the tool_dependencies.xml system. To do this the Tool Shed XML installation recipe now installs the same wrapper script clinod used in the BioConda package for calling the JAR file.

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 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/clinod/
...

or:

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

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only tools/clinod/
...
$ tar -tzf shed_upload.tar.gz
test-data/four_human_proteins.fasta
test-data/four_human_proteins.clinod-1.3.tabular
tools/clinod/README.rst
tools/clinod/clinod.xml
tools/clinod/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. Command line NoD is available and licenced separately.