Setting up NCBI Blast on Unix System
While installing a precompiled version of NCBI blast on your localbox is fairly straightforward, there are a few gotchas that got me. Let me eloborate in hopes that they won’t get you too.
If you’re following the instructions kindly provided at NCBI’s site, good. Continue. They’re quite adequate and will work for most. If you’re still reading this message, I take it the instructions were lacking.
One problem you might have is installing at database. I don’t know why, but the update_blastdb.pl script that is packaged with the binaries did nothing but waste my time. You can still download the gzipped files and install them yourself. I chose to go the NONFORMATED DB route because the preformated databases that I downloaded where missing some files. Formatting the databases is a simple task and can be done with the formatdb command.
NCBI recommends that you place your databases in a seperate directory. To let blastall, megablast, et al. know about the dbs you must place an .ncbirc file in your home directory or have one in the current working directory when you “blast” a sequence. If you don’t know who will be using the programs, you can tell blast where the databases are located with the “-d” flag.
megablast -d ../blast/db/nt -i myseq.fasta -o megaoutput.bls
It makes more sence to me to state the db path explicitly since you probably don’t want to make sure that every user has a .ncbirc file in their home directory (assuming this install is for a multi-user system). Explictly stating the db path also is helpful when calling the program from a script.
