On Tue, May 31, 2011 at 11:26 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> 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).

Apologies Alex, my memory was at fault - it was Peter van Heusden
(@pvanheus not @a_bossers):


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