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 

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:
> To:
> CC:
> 2012/3/21 Makis Ladoukakis <>:
> > 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
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