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:

ls 
/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/tool-data/blastdb/refseq_rna.*

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.

Peter

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to