On Tue, Jun 28, 2011 at 9:52 PM, George Michopoulos
<gior...@stanford.edu> wrote:
> Hey everyone,
> Hope all is well! I was wondering if someone could help me with
> another error I ran into. I recently downloaded the NCBI BLAST+ toolkit and
> it automatically installed itself into Galaxy. I'm just wondering if anyone
> knows where I am supposed to put the directory with the database files it
> needs to run correctly, or if it makes a difference.

It shouldn't matter as long a you use an appropriate path in the
blastdb.loc and blastdb_p.loc files. We use /data/blastdb/ for ours.

> I have configured the
> blastdb.loc file as shown below, and the database now appears in the
> drop-down menu for the NCBI tools, but when I try executing any of the
> BLASTs Galaxy returns the following error, regardless of the path
> permutation I try:

At least Galaxy is finding the loc file :)

> When I tried putting the databases within the galaxy installation (within
> galaxy_test) and I used the whole path:
> BLAST Database error: No alias or index file found for nucleotide
> database [/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/tool-data/blastdb/refseq_rna] in
> search path
> [/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/database/job_working_directory/28::]
> Return error code 2 from command: tblastx -query
> /Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/database/files/000/dataset_27.dat -db
> "/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/tool-data/blastdb/refseq_rna"
> -evalue 0.001 -out
> /Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/database/files/000/dataset_32.dat -outfmt
> 6 -num_threads 8

Does BLAST+ work at the command line?

Does BLAST+ work within Galaxy for FASTA vs FASTA (rather than
FASTA vs database)?

Also what does this give:


My guess is you have tried a valid path, but that the Galaxy user does
not have read permission so BLAST+ can't open the database.


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