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sourmash-bio / wort

A database for signatures of public genomic sources
https://wort.sourmash.bio
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update download code to use entrez-direct #59

Closed bluegenes closed 1 year ago

bluegenes commented 1 year ago

@luizirber - here's the edirect code we chatted about a few times, but actually in the right place, and verified that it downloads data that ~looks right.

Not sure how helpful this is, since I seem to recall there were a few other things that needed work.

I installed entrez-direct via conda:

name: edirect
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - entrez-direct>=16,<17
luizirber commented 1 year ago

Closed in favor of #60