Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ENH: action to get preformatted blast databases #135

Open
nbokulich opened this issue May 17, 2022 · 1 comment
Open

ENH: action to get preformatted blast databases #135

nbokulich opened this issue May 17, 2022 · 1 comment

Comments

@nbokulich
Copy link
Collaborator

NCBI hosts a database of preformatted blast databases, and a tool to download these programmatically (at the moment this seems to be a perl script, update_blastdb.pl, which ships with blast+).

It would be neat to add an action to RESCRIPt for downloading these databases (basically, this would allow quick validation of the source and timestamp in provenance).

One blocker at the moment is the lack of a BLASTDB type/format in Q2 — related to qiime2/q2-feature-classifier#158

@colinbrislawn
Copy link
Contributor

Direct link: https://ftp.ncbi.nlm.nih.gov/blast/temp/update_blastdb.pl

Not sure if we want to wrap this script or just port part of it

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants