I've CC'd the mailing list again (assuming you omitted it by
mistake - its easily done).
On Tue, Nov 9, 2010 at 8:43 PM, John David Osborne wrote:
>>I've written a BLAST+ wrapper which is now in galaxy-central, and
>>will eventually be in galaxy-dist and thus potentially on the public
>>Galaxy server (assuming it won't tax it too much). This doesn't
>>(yet) offer the option to run the BLAST remotely at the NCBI
>>(the wrapper could do this in theory). However, running a BLAST
>> against the NCBI databases will cause difficulties for reproducibility
>>(since we have no control over the databases, and the NCBI make
> Understood, I assume then most people get their sequence data
> and upload before starting a workload... That wrapper does sound
> handy though! It just seems odd to me that the Galaxy portal
> doesn't have a generic blast tool and standard (nt, nr, etc...) to
> run against.
Well, I'm sure they will consider it in future. But if I were in
their shoes, I'd be a little nervous about the computational
load it might impose.
>>Would you be running your own Galaxy server?
> That's the current plan. We are also looking at Taverna, but it
> doesn't seem like I can find much in the way (actually none)
> of biology publications that use it as part of their workflow. I
> haven't looked that hard though.
Within our institute we intend to offer BLAST running on our
departmental server (in Galaxy) for Biologists to run large
searches (e.g. multiple query sequences like a set of contigs)
against both NCBI databases like NR and also in house ones
(e.g. unpublished genomes), and as part of workflows (e.g.
upload a FASTA file, blast against organism X, divide the
FASTA file into those with good matches and those without).
This is drifting into a discussion more suited for the galaxy
dev mailing list though ;)