Mercurial > repos > peterjc > blast2go
view tools/blast2go/blast2go.txt @ 5:e4419efbefad draft
Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!
| author | peterjc |
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| date | Fri, 22 Feb 2013 08:47:27 -0500 |
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Galaxy wrapper for Blast2GO for pipelines, b2g4pipe =================================================== This wrapper is copyright 2011-2013 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 v2.5, 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 ============ The main dependency is b2g4pipe which must be installed manually. Also we strongly recommend installing a local Blast2GO database as well (see the intructions below about the blast2go.loc file). At the time of writing, the current version is b2g4pipe v2.5 which is available here: http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip 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/b2g4pipe_v2.5/blast2go.jar Installation of the Galaxy wrapper should work automatically via the Galaxy Tool Shed, including the dependency on 'blast_datatypes' for the 'blastxml' file format definition. To install the wrapper manually, first install 'blast_datatypes', then copy or move the following files under the Galaxy tools folder, e.g. in a tools/blast2go/ folder: * blast2go.xml (the Galaxy tool definition) * blast2go.py (the Python wrapper script) * blast2go.txt (this README file) For a manual installation of the wrapper 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="blast2go/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 is often out of date. The current server IP address and database name may given on the Blast2GO website, or can be found by running the latest GUI version via Java web-start, and looking under the tools/options menu. These property files can be anywhere accessable to the Galaxy Unix user, we put them with the JAR file etc. You must tell Galaxy about these Blast2GO property files so that they can be offered to the user. Copy file blast2go.loc.sample to tool-data/blast2go.loc under the Galaxy folder and edit this to match your installation. This must be plain text, tab separated, with three columns: (1) ID for the setup, e.g. Spain_2012_August (2) Description for the setup, e.g. Database in Spain (August 2012) (3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2012_August.properties Avoid including "Blast2GO" in the description (column 2) as this text 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. v0.0.3 - Include sample loc file, tool-data/blast2go.loc.sample v0.0.4 - Include repository_dependencies.xml file for 'blastxml' format (previously included in the core Galaxy installation) v0.0.5 - Quote arguments in case of spaces in filenames (internal change) - Last release supporting b2g4pipe v2.3.5 v0.0.6 - Support for b2g4pipe v2.5 instead of v2.3.5 - Now invoked with a class path and es.blast2go.prog.B2GAnnotPipe rather then simply calling the jar file - Now uses the switch -annot instead of -a (this change breaks support for b2g4pipe v2.3.5 unfortunately) - Catch a few error messages and treat them explicitly as errors. 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/blast2go/blast2go.xml tools/blast2go/blast2go.py tools/blast2go/blast2go.txt tools/blast2go/repository_dependencies.xml tool-data/blast2go.loc.sample Check this worked: $ tar -tzf blast2go.tar.gz tools/blast2go/blast2go.xml tools/blast2go/blast2go.py tools/blast2go/blast2go.txt tools/blast2go/repository_dependencies.xml tool-data/blast2go.loc.sample 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.