view blast_datatypes.txt @ 4:f9a7783ed7b6 draft

Uploaded v0.0.14 adding BLAST database support. See also the matching update for the NCBI BLAST+ wrappers which use these new definitions. This update included work by Edward Kirton.

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

These Galaxy datatypes are copyright 2010-2012 by Peter Cock, The James Hutton
Institute (formerly SCRI, Scottish Crop Research Institute), UK. 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.


History
=======

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

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)


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).


Developers
==========

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

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

$ tar -czf blast_datatypes.tar.gz blast_datatypes.txt datatypes_conf.xml blast.py

Check this worked:

$ tar -tzf blast_datatypes.tar.gz
blast_datatypes.txt
datatypes_conf.xml
blast.py

Note that the placement of these three files under tools/ncbi_blast_plus is
arbitrary - this just puts them next to the tool wrappers which use them.

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


Licence (MIT/BSD style)
=======================

Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted, provided that any copyright notices
appear in all copies and that both those copyright notices and this
permission notice appear in supporting documentation, and that the
names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software
without specific prior permission.

THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
OR PERFORMANCE OF THIS SOFTWARE.

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