view README.rst @ 9:e36c60d13c94 draft

Uploaded v0.0.18, tweak display_data for running tests

Galaxy datatypes for NCBI BLAST+ suite
======================================

These Galaxy datatypes are copyright 2010-2013 by Peter Cock, The James Hutton
Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
Contributions/revisions copyright 2012 Edward Kirton. All rights reserved.
Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved.

See the licence text below.

Note that these files (and the associated BLAST+ wrappers) were originally
distributed as part of the main Galaxy repository, but as of August 2012 moved
to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the
wrappers). My thanks to Dannon Baker from the Galaxy development team for his
assistance with this.

It is available from the Galaxy Tool Shed at:
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes


History
=======

These versions numbers initially matched those for 'ncbi_blast_plus', but are
not used explicitly in the datatypes themselves.

======= ======================================================================
Version Changes
------- ----------------------------------------------------------------------
v0.0.11 - Final revision as part of the Galaxy main repository, and the
          first release via the Tool Shed
v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
          (based on work by Edward Kirton)
v0.0.15 - Fixes a MetadataElement bug and includes more of the optional
          BLAST database files (contribution from Nicola Soranzo)
v0.0.16 - Adopt standard MIT License.
        - Use reStructuredText for this README file.
        - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
        - Nucleotide database definition aware of MegaBLAST index superheader
v0.0.17 - Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes
v0.0.18 - Add retries to BLAST XML merge code.
        - Modify display_data method to allow unit tests to function.
======= ======================================================================


Installation
============

Doing this automatically via the Galaxy Tool Shed is probably simplest.


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

Normally you would install this via the Galaxy ToolShed, which would move
the provided blast.py file into a suitable location and process the
datatypes_conf.xml entry to be combined with your local configuration.

However, if you really want to this should work for a manual install. Add
the following lines to the datatypes_conf.xml file in the Galaxy main folder::

    <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
    <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/>
    <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/>

and later in the sniffer section::

    <sniffer type="galaxy.datatypes.blast:BlastXml"/>

Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
the blast.py file provided in this tar-ball.  Finally add 'import blast' near
the start of file lib/galaxy/datatypes/registry.py (after the other import
lines).


Bug Reports
===========

You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev


Developers
==========

BLAST+ datatypes and wrappers, and other tools were originally developed on the
following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools

As of July 2013, development is continuing on a dedicated GitHub repository:
https://github.com/peterjc/galaxy_blast

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

    $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py

Check this worked::

    $ tar -tzf blast_datatypes.tar.gz
    README.rst
    datatypes_conf.xml
    blast.py

For development, rather than having a local ToolShed running, I currently
use a symlink from lib/galaxy/datatypes/blast.py to the actual file as
described above.


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

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

NOTE: This is the licence for the Galaxy BLAST datatypes **only**. BLAST+
and associated data files are available and licenced separately.