comparison tools/clinod/README.rst @ 5:9485cdfca57e draft

v0.0.8 internal changes

4:4d9a4a43861b

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

        - 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
==========

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)
=============

5:9485cdfca57e

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

        - 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.
v0.0.8  - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
======= ======================================================================


Developers
==========

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 --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/
    ...

or::

    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/
    ...

To just build and check the tar ball, use::

    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/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)
=============