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.00.phr /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.pin /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.pnd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.pni /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.pog /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.ppd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.ppi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.psd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.psi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.00.psq ... /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.phd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.phi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.phr /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.pin /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.pnd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.pni /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.pog /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.ppd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.ppi /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.psd /media/sf_mikeds_bioinf/GenbankDB_Files/nr/nr.10.psi /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