comparison tools/venn_list/README.rst @ 5:26e35d5133a1 draft

v0.0.9 - Tool Shed dependency for rpy and limma

4:991342eca214

Automated Installation
======================

This should be straightforward, Galaxy should automatically download the tool
and the Biopython dependency.

You will still need to install the R/Bioconductor package limma.


Manual Installation
===================

        - Tool definition now embeds citation information.
v0.0.8  - Reorder XML elements (internal change only).
        - Fixed and improved error handling when rpy is not available.
        - Test output relaxed to cope with more variation in PDF output.
        - Declare Biopython dependency via the Tool Shed.
======= ======================================================================


Developers
==========

http://bitbucket.org/peterjc/galaxy-central/src/tools

Development has now moved to a dedicated GitHub repository:
https://github.com/peterjc/pico_galaxy

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
the following command from the Galaxy root folder::

    $ tar -czf venn_list.tar.gz tools/venn_list/README.rst tools/venn_list/venn_list.* tools/venn_list/tool_dependencies.xml test-data/magic.pdf test-data/venn_list.tabular test-data/rhodopsin_proteins.fasta

Check this worked::

    $ tar -tzf venn_list.tar.gz
    tools/venn_list/README.rst
    tools/venn_list/venn_list.py
    tools/venn_list/venn_list.xml
    tools/venn_list/tool_dependencies.xml
    test-data/magic.pdf
    test-data/venn_list.tabular
    test-data/rhodopsin_proteins.fasta


Licence (MIT)
=============

5:26e35d5133a1

Automated Installation
======================

This should be straightforward, Galaxy should automatically download the tool
and the Python dependencies Biopython and rpy, and the R/Bioconductor package
limma.


Manual Installation
===================

        - Tool definition now embeds citation information.
v0.0.8  - Reorder XML elements (internal change only).
        - Fixed and improved error handling when rpy is not available.
        - Test output relaxed to cope with more variation in PDF output.
        - Declare Biopython dependency via the Tool Shed.
v0.0.9  - Test with three-way Venn diagram.
        - Includes testing of failure mode.
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
        - Tool Shed dependency for rpy and limma (thanks to Björn Grüning).
======= ======================================================================


Developers
==========

http://bitbucket.org/peterjc/galaxy-central/src/tools

Development has now moved to a dedicated GitHub repository:
https://github.com/peterjc/pico_galaxy

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 ~/repositories/pico_galaxy/tools/venn_list/
    ...

or::

    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/venn_list/
    ...

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

    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/venn_list/
    ...
    $ tar -tzf shed_upload.tar.gz 
    tools/venn_list/README.rst
    tools/venn_list/tool_dependencies.xml
    tools/venn_list/venn_list.py
    tools/venn_list/venn_list.xml
    test-data/magic.pdf
    test-data/rhodopsin_proteins.fasta
    test-data/venn_list.tabular


Licence (MIT)
=============