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.cock@googlemail.com> wrote:

On Wed, Mar 19, 2014 at 6:42 AM, Nilaksha Neththikumara
<nilakshafreezon@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 ;)