On Tue, Nov 9, 2010 at 7:42 PM, John David Osborne <ozborn@uab.edu> wrote:

Hi,

I am new to galaxy and I am wondering if it is possible to:

1) Fetch data from NCBI from the main galaxy portal? I assume this is possible from a local installation. For example, do a query say looking for a disease in rodents using Ratmine, export to Galaxy (did this fine) and then use the returned identifies to fetch sequence from NCBI. I can't seem to do this last bit - I don't even see NCBI under "Get Data".

I'd guess a wrapper for NCBI Entrez efetch could be written (if there isn't one already).

2) Run blast from the main galaxy portal? Is this disabled due to too many users? Does this option appear once you have sequence?

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 regular updates).

The context is our group at UAB is evaluating galaxy and I am just playing around to see what it can do.

Would you be running your own Galaxy server? Peter