Galaxy is a web-based platform for biological data analysis, supporting extension with additional tools (often wrappers for existing command line tools) and datatypes. See http://www.galaxyproject.org/ and the public server at http://usegalaxy.org for an example.
The NCBI BLAST suite is a widely used set of tools for biological sequence comparison. It is available as standalone binaries for use at the command line, and via the NCBI website for smaller searches. For more details see http://blast.ncbi.nlm.nih.gov/Blast.cgi
This repository is for the development of the main Galaxy wrappers for the NCBI BLAST+ suite, associated datatype definitions for use within Galaxy, and dependency handling within the Galaxy Tool Shed framework.
It also contains additional related Galaxy tools for working with BLAST.
The main focus of this work is the development of the NCBI BLAST+ command line tool wrappers and datatype definitions for Galaxy, published on the Galaxy Tool Shed here:
- http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
- http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes/
Development test releases are on the Test Tool Shed here:
- http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/
- http://testtoolshed.g2.bx.psu.edu/view/devteam/blast_datatypes/
The NCBI BLAST+ binaries were initially included within the Galaxy wrappers (ncbi_blast_plus), but are now handled as Tool Shed packages:
- http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
- http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
- http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_27
- http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_27
- http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_28
- http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_28
- http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_29
- http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_29
Note this targets the NCBI's C++ rewrite of BLAST called BLAST+, available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ -- we do not support the now deprecated "legacy" BLAST suite written in C, still available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/
These Galaxy BLAST+ wrappers were originally written by Peter Cock and were incorporated into https://bitbucket.org/galaxy/galaxy-central/ the main Galaxy repository on BitBucket in September 2009, where they were maintained via pull requests and patches from Peter's repository fork: https://bitbucket.org/galaxy/galaxy-central/
In August 2010 Dannon Baker from the Galaxy Team migrated the BLAST+ tools and datatypes to the Galaxy Tool Shed (links above). This was part of a long term plan to move most tools out of the main Galaxy repository. Development of the wrappers continued on the 'tools' branch of Peter's Galaxy fork on BitBucket with additional contributions via patches and pull requests.
Recognising the growing number of potential contributors, an informal "Birds of a Feather" (BoF) http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyBlast meeting was held in July 2013 during the annual Galaxy Community Conference. It was agreed to move the code into a dedicated Git repository on GitHub, with the goal of giving the project a clearer identity and making it easier for Peter to manage.
This repository also contains other BLAST related Galaxy tools, some already available on the Galaxy Tool Shed:
- http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
- http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
Any development test releases are on the Test Tool Shed, for example:
- http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
- http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
Within the tools folder is one folder for each Tool or Tool Suite released
on the Galaxy Tool Shed. Similarly, dependencies contains packages for
Galaxy Tool Shed dependency definitions, and datatypes contains packages
for Galaxy Tool Shed datatype definitions.
Additionally there is a shared test-data folder used for functional test
sample data, and a shared tool-data folder used for configuration files.
Most of these Galaxy tools include a <tests> section in the tool XML files,
which defines one or more functional tests - listing sample input files and
user parameters, along with the expected output. If you install the tools,
you can run these tests via Galaxy's run_functional_tests.sh script -
and/or do this automatically if installing the tools via the Tool Shed.
The Galaxy team run nightly tests on all the tools which have been uploaded to the main Tool Shed and the Test Tool Shed, simulating how they would behave in a local Galaxy instance once installed via the Tool Shed.
In addition we are running the same functional tests via TravisCI whenever this GitHub repository is updated:
This TravisCI integration simulates a manual install of these Galaxy Tools
and their dependencies. See the special .travis.yml file for more
technical details.
You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
Please see the README file in each folder, but by default the MIT license is being used.