Computing - Install NCBI nr nt BLAST Database on Mox

2018
Miscellaneous
Author

Sam White

Published

November 14, 2018

Per this issue on GitHub, I installed the pre-formatted NCBI non-redudant (nr) nucleotide (nt) database on Mox.

Database was downloaded from here:

Database is installed in the following location on Mox:

Here’re the commands used to download and setup the database files:

Login Node

Create directories, download files (should’ve used the –no-directories option), move files to correct directory and remove unnecessary folders/files.

mkdir /gscratch/srlab/blastdbs
mkdir /gscratch/srlab/blastdbs/ncbi-nr-nt-20181114
cd /gscratch/srlab/blastdbs/ncbi-nr-nt-20181114
wget --recursive --no-parent --accept "nt.*tar.gz" ftp://ftp.ncbi.nlm.nih.gov/blast/db
cd ftp.ncbi.nlm.nih.gov/blast/db
mv *.gz /gscratch/srlab/blastdbs/ncbi-nr-nt-20181114
cd /gscratch/srlab/blastdbs/ncbi-nr-nt-20181114
rm -rf ftp.ncbi.nlm.nih.gov

Build Node

Unpack gzipped tarballs.

for i in *.gz; do tar -xzvf $i; done