Hi all,
As I mentioned on Twitter, at the end of last week I wrapped Blast2GO for Galaxy, using the b2g4pipe program (Blast2GO for pipelines). See http://blast2go.org/
Currently current code is on bitbucket under my tools branch, https://bitbucket.org/peterjc/galaxy-central/src/tools/
Specifically files tools/ncbi_blast_plus/blast2go.* viewable here: https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/ncbi_blast_plus...
I've using a Galaxy location file, tool-data/blast2go.loc, to offer one or more Blast2GO configurations (properties files), mapping this to the -prop argument. This way you could have for example the Spanish Blast2GO server with its current database (May 2010), and a local Blast2GO database. I want to setup a local database and try this before submitting the wrapper to the Tool Shed.
The input to the tool is a BLAST XML file, specifically blasting against a protein database like NR (so blastp or blastx, not blastn etc). I want to try some very large BLAST XML files to confirm b2g4pipe copes with the current BLAST+ output files - I gather there were some problems in this area in the past, so having the wrapper script fragment the XML might be a workaround. Currently the only real function of the wrapper script is to rename the output file - b2g4pipe insists on using the *.annot extension.
Right now the only output is a tabular three column *.annot file, which can be loaded into the Blast2GO GUI. For analysis within Galaxy, I'm wondering about an option to split the first column (which holds the original FASTA query's identifier and any description) in two. i.e. Split at the first white space to give the FASTA identifier, and any optional description as a separate column. That would make linking/joining/filtering on the ID much easier.
If anyone has any comments or feedback now, that would be welcome. Yesterday Alex Bossers indicated on Twitter that Gerrit had also been looking at this (CC'd).
Regards,
Peter