view tools/ncbi_blast_plus/blast2go.txt @ 1:0f159cf346c8

Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository

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

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

This is a wrapper for the command line Java tool b2g4pipe v2.3.5,
Blast2GO for pipelines. See:

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

A. Conesa and S. Götz.
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
Int. J. Plant Genomics. 619832, 2008.
http://dx.doi.org/10.1155/2008/619832

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

http://www.blast2go.org/



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

You can change the path by editing the definition near the start of the Python
script blast2go.py, but by default it expects the underlying tool to be here:

/opt/b2g4pip/blast2go.jar

To install the wrapper copy or move the following files under the Galaxy tools
folder, e.g. in the tools/ncbi_blast_blast folder:

* blast2go.xml (the Galaxy tool definition)
* blast2go.py (the Python wrapper script)
* blast2go.txt (this README file)

You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
tool. We suggest putting it next to the NCBI BLAST+ wrappers. Just add the line:

<tool file="ncbi_blast_plus/blast2go.xml" />

As part of setting up b2g4pipe you will need to setup one or more Blast2GO
property files which tell the tool which database to use etc. The example
b2gPipe.properties provided with b2g4pipe v2.3.5 is out of date, with the
latest server IP address and database name given on the Blast2GO website.
These files can be anywhere accessable to the Galaxy Unix user, we put them
under /opt/b2g4pipe with the JAR file etc.

You must tell Galaxy about these Blast2GO property files so that they can be
offered to the user. Create the file tool-data/blast2go.loc under the Galaxy
folder. This must be plain text, tab separated, with three columns:

(1) ID for the setup, e.g. Spain_2010_May
(2) Description for the setup, e.g. Database in Spain (May 2010)
(3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2010_May.properties

Avoid including "Blast2GO" in the description (column 2) as this will be
included in the automatically assigned output dataset name. The blast2go.loc
file allows you to customise the database setup. If for example you have a local
Blast2GO server running (which we recommend for speed), and you want this to be
the default setting, include it as the first line in your blast2go.loc file.

Consult the Blast2GO documentation for details about the property files and
setting up a local MySQL Blast2GO database.


History
=======

v0.0.1 - Initial public release
v0.0.2 - Documentation clarifications, e.g. concatenated BLAST XML is allowed.
       - Fixed error handler in wrapper script (for when b2g4pipe fails).
       - Reformats the XML to use old NCBI-style concatenated BLAST XML since
         b2g4pipe crashes with heap space error on with large files using
         current NCBI output.


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:

$ tar -czf blast2go.tar.gz tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt

Check this worked:

$ tar -tzf blast2go.tar.gz
tools/ncbi_blast_plus/blast2go.xml
tools/ncbi_blast_plus/blast2go.py
tools/ncbi_blast_plus/blast2go.txt


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. Blast2GO and
associated data files are available and licenced separately.