On Tue, Apr 30, 2013 at 3:56 AM, Mike Dyall-Smith mike.dyallsmith@gmail.com wrote:
This follows on from Kenneth Auerbach's question Sep 12, 2012: Galaxy error running NCBI BLAST: blastx http://dev.list.galaxyproject.org/Galaxy-error-running-NCBI-BLAST-blastx-td4...
I wish to use a local copy of the genbank database for searches. The genbank db files are sitting in a folder on an external drive, and I have altered the blastdb_p.loc to point to them.
I can see and select this database within galaxy, but when I try using blast+ blastp tool, I get the error ""BLAST Database error: No alias or index file found for protein database [/media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr] in search path [/var/lib/galaxy-server/database/job_working_directory]
As suggested previously by Peter Cock, I can list all the files with: ls /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr* which gives me the list: /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.phd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.phi ... /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.psq /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.pal
The alias file, nr.pal is the last one in the list above, so is present.
I changed the default directory for the blast database: BLASTDB=/media/sf_mikeds_bioinf/GenbankDB_Files/nr
- this made no difference to the error.
I am running biolinux 7 (latest) in ubuntu within VirtualBox, on a macbook pro. The external drive is a shared folder, and I can see all the files within galaxy (e.g. I can import data data files).
Any help would be appreciated.
Regards, Mike DS
Hi Mike,
Have you been able to successfully run blastp with the nr database at the command line by hand?
Could you share the (relevant lines from) your blastdb_p.loc file, and the matching error message from blastp when called from Galaxy?
With your files here, /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.* you should use /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr as the BLAST the database name (column 3 in blastdb_p.loc for use in Galaxy).
(Personally I don't bother with the BLASTDB setting, it is just one more point of confusion when using BLAST on a cluster.)
Regards,
Peter