diff tools/clinod/README.rst @ 3:6a9debe4b860 draft

Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub

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+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.