sdwfrost / ncbi-blast-dbs Goto Github PK

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 and is thus not as universal.

gem install ncbi-blast-dbs

If md5sum command is not present, you can install it using Homebrew:

brew install md5sha1sum

ncbi-blast-dbs

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