setting up local database

sequenceserver
#1

I’m trying to set up sequenceserver.

The following happens

"[theo-kirklands-macbook-pro:~] theoneal% sequenceserver

Database dir not set.

SequenceServer needs to know where your FASTA files or BLAST+ databases are.
Please enter the path to the relevant directory (default: current directory).

Press Ctrl+C to quit.

blast/db
Error obtaining BLAST databases.
Tried: blastdbcmd -recursive -list /Users/theoneal/blast/db -list_outfmt “%f %t %p %n %l %d”
Error:
BLAST Database error: Could not find volume or alias file (nr.01) referenced in alias file (/Users/theoneal/blast/db/nr.00/nr)."

I get the same error message when I try to use the ncbi-blast-2.2.30+ stand alone blast. There is a nr.pal file in the nr folder (575 bytes) and a nt.nal file (0 bytes) in the nt folder. Bothe nr and nt folders are in the db folder.

Any ideas?

Thanks

Theo

#2

Looks like you only have alias files (nal/pal) but not the volumes, or somehow the path to the volumes in the alias files don’t match the location of the volumes. The alias file is a simple text file that you can edit to indicate the path to the volumes, or you can move the volumes back to the folder containing the alias file, or download the volumes — whichever is the case.

— Priyam