comparison tools/protein_analysis/README.rst @ 20:a19b3ded8f33 draft

v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes

19:f3ecd80850e2

(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
See the included LICENCE file for details (MIT open source licence).

The wrappers are available from the Galaxy Tool Shed
http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 

Citation
========

If you use any of these Galaxy tools in work leading to a scientific

        - Use reStructuredText for this README file.
        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
v0.2.6  - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
        - Updated the ``suite_config.xml`` file (overdue).
        - Tool definition now embeds citation information.
v0.2.7  - Style cleanup in Python scripts.
v0.2.8  - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
        - Record version of Promoter 2 via ``<version_command>``.
v0.2.9  - Further style cleanup in Python scripts (internal change only).
======= ======================================================================


Developers
==========

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/protein_analysis/
    ...

or::

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

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

    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/protein_analysis/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/Adenovirus.fasta
    test-data/Adenovirus.promoter2.tabular
    test-data/empty.fasta
    test-data/empty_promoter2.tabular
    test-data/empty_psortb_terse.tabular

20:a19b3ded8f33

(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
See the included LICENCE file for details (MIT open source licence).

The wrappers are available from the Galaxy Tool Shed
http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp

Citation
========

If you use any of these Galaxy tools in work leading to a scientific

        - Use reStructuredText for this README file.
        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
v0.2.6  - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
        - Updated the ``suite_config.xml`` file (overdue).
        - Tool definition now embeds citation information.
v0.2.7  - Style cleanup in Python scripts using ``pep8``.
v0.2.8  - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
        - Record version of Promoter 2 via ``<version_command>``.
v0.2.9  - Further style cleanup in Python scripts (internal change only).
v0.2.10 - Style cleanup in Python scripts using ``flake8``.
        - Record TMHMM and SignalP wrapper version via ``<version_command>``.
        - Python 3 compatible print function and exception handling.
        - Python 3 compatible subprocess calling.
        - Removed obsolete ``suite_config.xml`` file.
v0.2.11 - Updated RXLR tool dependencies to get HMMER2 via BioConda.
        - Use ``<command detect_errors="aggressive">`` (internal change only).
        - Single quote command line arguments (internal change only).
        - Record WoLF PSORT wrapper version via ``<version_command>``.
        - Fix error handling in SignalP wrapper.
        - Record SignalP version via ``<version_command>``.
        - Internal job splitter will skip starting any pending jobs after a
          child job fails (so the entire task will error out more quickly).
======= ======================================================================


Developers
==========

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/protein_analysis/
    ...

or::

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

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

    $ planemo shed_upload --tar_only tools/protein_analysis/
    ...
    $ tar -tzf shed_upload.tar.gz
    test-data/Adenovirus.fasta
    test-data/Adenovirus.promoter2.tabular
    test-data/empty.fasta
    test-data/empty_promoter2.tabular
    test-data/empty_psortb_terse.tabular