Fast download BLAST databases from NCBI
Database files (volumes) are downloaded in parallel: number of threads to use is determined automatically. MD5 checksum is verified and the database volume extracted upon download. Database volumes are not downloaded in a particular order. The volumes are updated if a newer version is available on the server, or re-downloaded if corrupt. Aborted downloads are safely resumed.
ncbi-blast-dbs is faster than NCBI's update_blastdb.pl. But unlike
update_blastdb.pl, which is a pure Perl script, ncbi-blast-dbs delegates
download and checksum verification to wget and md5sum / md5 and is thus
not as universal.
Installation
gem install ncbi-blast-dbs
Usage
List available BLAST databases
ncbi-blast-dbs
Download all volumes of a BLAST database
ncbi-blast-dbs nt nr
Databases are downloaded one after the other. Volumes of each database are downloaded in parallel. Downloads are placed in the current directory.
NCBI expects users to submit their email address when downloading data from their FTP server. To comply with that, download as:
email="my email address here" ncbi-blast-dbs nr