comparison tools/clinod/README.rst @ 4:4d9a4a43861b draft

Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.

3:6a9debe4b860

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

        - 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
==========

4:4d9a4a43861b

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

    $ ./run_tests.sh -id clinod

That's it.


History

        - 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
v0.0.7  - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
        - Tool definition now embeds citation information.
======= ======================================================================


Developers
==========