Galaxy wrappers for NCBI BLAST+ suite
=====================================

These wrappers 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.

Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+),
and do not work with the NCBI 'legacy' BLAST suite (e.g. blastall).

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


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

For those not using Galaxy's automated installation from the Tool Shed, put
the XML and Python files under tools/ncbi_blast_plus and add the XML files
to your tool_conf.xml as normal.

You must tell Galaxy about any system level BLAST databases using configuration
files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein
databases like NR).

You will also need to install 'blast_datatypes' from the Tool Shed. This
defines the BLAST XML file format ('blastxml').


History
=======

v0.0.11 - Final revision as part of the Galaxy main repository, and the
          first release via the Tool Shed
v0.0.12 - Implements genetic code option for translation searches.
        - Changes <parallelism> to 1000 sequences at a time (to cope with
          very large sets of queries where BLAST+ can become memory hungry)
        - Include warning that BLAST+ with subject FASTA gives pairwise
          e-values
v0.0.13 - Use the new error handling options in Galaxy (the previously
          bundled hide_stderr.py script is no longer needed).


Developers
==========

This script and related 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 root folder:

$ ./tools/ncbi_blast_plus/make_ncbi_blast_plus.sh

This similifies ensuring a consistent set of files is bundled each time,
including all the relevant test files.


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 Wrapper only. BLAST+ and
associated data files are available and licenced separately.