comparison tools/blast2go/README.rst @ 10:8664c4c94764 draft default tip

v0.0.11 - Assorted packaging updates (overdue upload)

9:887adf823bc0

Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
===================================================

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 (MIT licence).

This is a wrapper for the command line Java tool b2g4pipe v2.5, Blast2GO for
pipelines, currently a free to use download available at:

Please cite the following papers:

Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
http://dx.doi.org/10.7717/peerj.167

S. Geotz et al. (2008).
High-throughput functional annotation and data mining with the Blast2GO suite.
Nucleic Acids Res. 36(10):3420-3435.
http://dx.doi.org/10.1093/nar/gkn176

A. Conesa and S. Geotz (2008).
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
International Journal of Plant Genomics. 619832.
http://dx.doi.org/10.1155/2008/619832

A. Conesa et al. (2005).
Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
Bioinformatics 21:3674-3676.
http://dx.doi.org/10.1093/bioinformatics/bti610

See also http://www.blast2go.com/


Automated Installation

        - Split out ``massage_xml_for_blast2go.py`` as a standalone file.
v0.0.9  - Update README file now that BioBam are selling the latest version
          of the Blast2GO command line tool. For now b2g4pipe v2.5 is still
          available as a free download.
        - Tool definition now embeds citation information.
v0.0.10 - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
======= ======================================================================


Developers
==========

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

    $ planemo shed_upload --tar_only  ~/repositories/galaxy_blast/tools/blast2go/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/blastp_sample.blast2go.tabular
    test-data/blastp_sample.xml
    tool-data/blast2go.loc.sample
    tools/blast2go/README.rst
    tools/blast2go/blast2go.py

10:8664c4c94764

Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
===================================================

This wrapper is copyright 2011-2017 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below (MIT licence).

This is a wrapper for the command line Java tool b2g4pipe v2.5, Blast2GO for
pipelines, currently a free to use download available at:

Please cite the following papers:

Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
https://doi.org/10.7717/peerj.167

S. Geotz et al. (2008).
High-throughput functional annotation and data mining with the Blast2GO suite.
Nucleic Acids Res. 36(10):3420-3435.
https://doi.org/10.1093/nar/gkn176

A. Conesa and S. Geotz (2008).
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
International Journal of Plant Genomics. 619832.
https://doi.org/10.1155/2008/619832

A. Conesa et al. (2005).
Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
Bioinformatics 21:3674-3676.
https://doi.org/10.1093/bioinformatics/bti610

See also http://www.blast2go.com/


Automated Installation

        - Split out ``massage_xml_for_blast2go.py`` as a standalone file.
v0.0.9  - Update README file now that BioBam are selling the latest version
          of the Blast2GO command line tool. For now b2g4pipe v2.5 is still
          available as a free download.
        - Tool definition now embeds citation information.
v0.0.10 - Python 3 ready
        - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
v0.0.11 - Fix parameter help text which was not being displayed.
        - PEP8 style updates to the Python script (internal change only).
        - Use ``<command detect_errors="aggressive">`` (internal change only).
        - Single quote command line arguments (internal change only).
        - Python 3 compatible syntax.
        - Record ``b2g4pipe_v2.5.zip`` SHA256 checksum, and download this via
          the Galaxy package cache.
======= ======================================================================


Developers
==========

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

    $ planemo shed_upload --tar_only  ~/repositories/galaxy_blast/tools/blast2go/
    ...
    $ tar -tzf shed_upload.tar.gz
    test-data/blastp_sample.blast2go.tabular
    test-data/blastp_sample.xml
    tool-data/blast2go.loc.sample
    tools/blast2go/README.rst
    tools/blast2go/blast2go.py