On Tue, Jun 28, 2011 at 9:52 PM, George Michopoulos giorgos@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