BOL: ncbi-datasets-cli -- Quickstart: command line tools !

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ncbi-datasets-cli -- Quickstart: command line tools !

ncbi-datasets-cli -- Quickstart: command line tools !

By Jit 1082 days ago Comments (1)

https://www.ncbi.nlm.nih.gov/datasets/docs/v1/quickstarts/command-line-tools/

Install and use the NCBI Datasets command line tools

The NCBI Datasets datasets command line tools are datasets and dataformat .

Use datasets to download biological sequence data across all domains of life from NCBI.

Use dataformat to convert metadata from JSON Lines format to other formats.

Conda download:

https://anaconda.org/conda-forge/ncbi-datasets-cli

Buld Download

https://www.ncbi.nlm.nih.gov/datasets/builder/?tax_id=29979

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- Jit@jit.aber
Jit 1082 days ago
(base) [jnarayan@hn1 TOOLS]$ curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 13.8M 100 13.8M 0 0 440k 0 0:00:32 0:00:32 --:--:-- 425k
(base) [jnarayan@hn1 TOOLS]$ curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/dataformat'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 11.4M 100 11.4M 0 0 509k 0 0:00:23 0:00:23 --:--:-- 558k
(base) [jnarayan@hn1 TOOLS]$ chmod +x datasets dataformat