Command line tools

Download and install the NCBI Datasets command line tools

Command line tools

Download and install the NCBI Datasets command line tools

The NCBI 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.

For more information about our tools, please refer to our How-to guides.

Datasets schema diagram



Note: The NCBI Datasets command line tools are updated frequently to add new features, fix bugs, and enhance usability. Command syntax is subject to change. Please check back often for updates.

Install NCBI Datasets command line tools

The NCBI Datasets command line tools are available on multiple platforms. To download previous versions of datasets and dataformat, please refer to the Download and Install page in the CLI v13 documentation.

SystemArchitectureDownload
LinuxAMD64
macOSUniversal
Windows (64-bit)AMD64
LinuxARM64
LinuxARM (32-bit)

Install using conda

The NCBI Datasets command line tools are available as a conda package. It includes both datasets and dataformat.

First, create a conda environment: conda create -n ncbi_datasets

Then, activate your new environment: conda activate ncbi_datasets

Finally, install the datasets conda package: conda install -c conda-forge ncbi-datasets-cli

Install using curl

Linux

Download datasets: curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets'
Download dataformat: curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/dataformat'
Make them executable: chmod +x datasets dataformat

macOS

Download datasets: curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/mac/datasets'
Download dataformat: curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/mac/dataformat'
Make them executable: chmod +x datasets dataformat

Windows

Download datasets: curl -o datasets.exe "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/win64/datasets.exe"
Download dataformat: curl -o dataformat.exe "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/win64/dataformat.exe"

Generated January 25, 2023