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Repository 'blast2go'
http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
blast2go
unrestricted
Maps BLAST results to GO annotation terms
Galaxy wrapper for Java command line tool Blast2GO for pipelines, b2g4pipe v2.5, available from http://blast2go.org/

The tool takes a single BLAST XML file as input, searched against a protein database such as the NCBI non redundant database (NR). The tool gives a single tabular output file, the annotation file which can be opened with the Blast2GO GUI.

The wrapper uses a Galaxy loc file to allow the use of one or more Blast2GO property files (e.g. different versions of the database, or different servers, or different evidence weighting settings). We use this to offer both a local Blast2GO database (fast) and the public database hosted in Valencia, Spain.
7:0ac3ef59ea93
peterjc
True
386

Repository README files - may contain important installation or license information

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 (MIT licence).

This is a wrapper for the command line Java tool b2g4pipe v2.5, Blast2GO for pipelines. It is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go

References

Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 http://dx.doi.org/10.7717/peerj.167

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

A. Conesa and S. Geotz (2008). Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. International Journal of Plant Genomics. 619832. http://dx.doi.org/10.1155/2008/619832

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

See also http://www.blast2go.com/

Automated Installation

Installation via the Galaxy Tool Shed should take care of the Galaxy side of things, including the dependency on 'blast_datatypes' which defines the 'blastxml' file format. However, you will also probably need to configure the Blast2GO property file(s), for example if you have a local Blast2GO database (which we recommend for speed).

Manual 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:

You can change the path by setting the B2G4PIPE environement variable to the desired folder, but by default the script looks for the JAR file here:

/opt/b2g4pipe_v2.5/blast2go.jar

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)
  • massage_xml_for_blast2go.py (Python XML reformatting script)
  • README.rst (this 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" />

If you wish to run the unit tests, also add this to tools_conf.xml.sample and move/copy the test-data files under Galaxy's test-data folder. Then:

$ ./run_functional_tests.sh -id blast2go

Configuration

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. Spain_2012_August.properties relative to the main JAR file, or with a full path 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

Version Changes
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.
v0.0.7
  • Update output description in XML file (b2g4pipe v2.3.5 included the sequence description, b2g4pipe v2.5 omits this).
v0.0.8
  • Automated installation via the Galaxy Tool Shed.
  • Added unit test.
  • Explain how to load the tabular file into the Blast2GO GUI.
  • Link to Tool Shed added to help text and this documentation.
  • Switch to standard MIT licence.
  • Use reStructuredText for this README file.
  • Updated citation information (Cock et al. 2013).
  • Development moved to GitHub, https://github.com/peterjc/galaxy_blast
  • Split out massage_xml_for_blast2go.py as a standalone file.

Developers

This script and related tools were originally developed on the 'tools' branch of the following BitBucket Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/

As of September 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 Galaxy root folder:

$ tar -czf blast2go.tar.gz blast2go/README.rst blast2go/blast2go.xml blast2go/blast2go.py blast2go/massage_xml_for_blast2go.py blast2go/repository_dependencies.xml blast2go/tool_dependencies.xml tool-data/blast2go.loc.sample test-data/blastp_sample.xml test-data/blastp_sample.blast2go.tabular

Check this worked:

$ tar -tzf blast2go.tar.gz
blast2go/README.rst
blast2go/blast2go.xml
blast2go/blast2go.py
blast2go/massage_xml_for_blast2go.py
blast2go/repository_dependencies.xml
blast2go/tool_dependencies.xml
tool-data/blast2go.loc.sample
test-data/blastp_sample.xml
test-data/blastp_sample.blast2go.tabular

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

Dependencies of this repository

Repository blast_datatypes revision de11e1a921c4 owned by devteam

Name Version Type
b2g4pipe 2.5 package

Contents of this repository

Name Description Version
Blast2GO Maps BLAST results to GO annotation terms 0.0.8

Automated tool test results

Time tested: 2014-04-17 05:50:17
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13085:c05752549163
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: blast2go
Tool version: blast2go
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.8)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu blast_datatypes devteam de11e1a921c4
TypeNameVersion
b2g4pipe package 2.5
Installation directory
/ToolDepsMain/b2g4pipe/2.5/peterjc/blast2go/0ac3ef59ea93
Time tested: 2014-04-16 05:44:42
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13065:1ad62c772728
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: blast2go
Tool version: blast2go
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.8)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu blast_datatypes devteam de11e1a921c4
TypeNameVersion
b2g4pipe package 2.5
Installation directory
/ToolDepsMain/b2g4pipe/2.5/peterjc/blast2go/0ac3ef59ea93
Time tested: 2014-04-15 06:19:26
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13058:1165a5a1221a
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: blast2go
Tool version: blast2go
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.8)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu blast_datatypes devteam de11e1a921c4
TypeNameVersion
b2g4pipe package 2.5
Installation directory
/ToolDepsMain/b2g4pipe/2.5/peterjc/blast2go/0ac3ef59ea93
Time tested: 2014-04-14 05:41:47
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13041:b423b847f58e
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: blast2go
Tool version: blast2go
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.8)
Tool shedNameOwnerChangeset revision
toolshed.g2.bx.psu.edu blast_datatypes devteam de11e1a921c4
TypeNameVersion
b2g4pipe package 2.5
Installation directory
/ToolDepsMain/b2g4pipe/2.5/peterjc/blast2go/0ac3ef59ea93

Categories
Ontology Manipulation
Sequence Analysis