Thanks a lot for the information. :) I'm new to the field so get confused at times. I started downloading the NCBI databases locally, but I have two questions.
1) There is no proper updating process for the locally installed NCBI databases. (according to my knowledge) So it seems I have to re download the database totally if I need to get them updated. And those databases are almost always being updating. (.sigh) 2) After installing databases, is there a particular way to let galaxy know where are my databases located? So that they can be included in the drop down menu of the blast+ wrappers for me to select :) Thanks a lot in advance Nilaksha Neththikumara. On Wed, Mar 19, 2014 at 3:33 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > On Wed, Mar 19, 2014 at 6:42 AM, Nilaksha Neththikumara > <nilakshafree...@gmail.com> wrote: > > Hello all, > > > > The newly developed blast+ wrappers seem to be very useful, but it seems > > like they do not contain the function to blast against remote servers > > instead of installing the databases locally. > > Am I missing something there? I need to do a remote search for a sequence > > within galaxy instance so I can automate the process. > > Help is much appreciated. > > > > Thanks a lot, > > Nilaksha > > Hi Nilaksha, > > You are correct, the BLAST+ wrappers for Galaxy don't currently > support the -remote option to connect to the NCBI over the > internet to run the searches there - we've talked about this > though, and I've filed an issue to track this in future: > https://github.com/peterjc/galaxy_blast/issues/39 > > What do you mean by you need remote search for automation? > You can download all the NCBI managed databases like NT/NR > locally, so most tasks can be done without the -remote option. > > Peter > > P.S. The BLAST+ wrappers aren't 'newly developed', work > started way back in 2011 ;) >
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