Dear Peter, Thank you for your reply. You are right I do have all 6 parts of the nr database on the server plus the .pal file in the same directory. The .loc file still is: database [build data] path nr_01_Mar_2012 nr 15 Mar 2012 /path/on/the/server/nr_directory/nr but the megablast tool still doesn't recognise the database. Am I missing something? Thank you in advance, Makis Ladoukakis
Date: Wed, 21 Mar 2012 10:21:16 +0000 Subject: Re: [galaxy-user] Trouble with BLAST+ and .loc file From: p.j.a.cock@googlemail.com To: makis4ever@hotmail.com CC: galaxy-user@lists.bx.psu.edu
2012/3/21 Makis Ladoukakis <makis4ever@hotmail.com>:
Dear Galaxy users,
I have been trying to upload a blastable database in my local instance of galaxy. I have used the nr database and generated all the nhr, nin, nsq, and nal files. I have also edited the blastdb.loc file in the galaxy-dist/tool-data/ directory and it looks like this:
database [build data] path nr_01_Mar_2012 nr 15 Mar 2012 /home/user/Desktop/nr.00/nr
Nevertheless when i start galaxy the megablast tool can't recognise the database. Am I missing something?
The NR database comes split up into many parts, 00 to 06 currently, and you need to download them all. They are linked by the nr.pal file, which you should also have downloaded. The database is then used via the full name of the nr.pal file (but without the .pal extension).
If you are running Galaxy on a server, it is likely your systems administrator can/has setup a shared set of NCBI BLAST databases for all the system users (including Galaxy), to avoid unnecessary copies under /home
Note that queries about local Galaxy installations are normally handled via the galaxy-dev mailing list (although perhaps the project needs three lists now given local Galaxy installations are getting more common and not everyone wants to follow the Galaxy development itself).
Peter