Hi Peter, I think a separate loc file for proteins makes sense, easier to maintain
backward compatibility that way. Only speaking for myself though.
On Sep 20, 2010, at 5:55 AM, Peter wrote:
On Thu, Sep 9, 2010 at 11:29 AM, Peter
> Hi all,
> Something I expect to find useful in several analysis pipelines is
> a Galaxy wrapper for the NCBI BLAST+ tools (or even the old
> NCBI "legacy" BLAST tools if such a wrapper exists).
> I've been looking over the tools in galaxy-dist and galaxy-central and
> the only NCBI BLAST wrapper I can see is for MEGABLAST, under
> Is there some more general NCBI BLAST+ wrappers that I have
> missed? Or is anyone already working on this?
I met Björn Grüning (CC'd) from the University of Freiburg
Pharmaceutical Bioinformatics at a workshop last week, and
they had a few simple BLAST+ wrappers setup. If I recall
correctly, all their databases were nucleotide databases.
For configuration, Björn re-used the existing blastdb.loc file
that comes with Galaxy for the NGS megablast_wrapper tool.
However, that (currently) only holds nucleotide BLAST
databases - and we would need to have separate lists for
nucleotide, protein, and RPS-BLAST protein domain databases.
I would suggest either:
(a) Add new loc files specific to proteins and rpsblast
(b) Extend the blastdb.loc format to include a fourth column
giving the database type (which can default to nucleotide).
What would the Galaxy team prefer?
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