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 ;)