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Getting started with the ElemBio CLI

Install the ElemBio CLI, authenticate, and run your first commands.

The ElemBio™ CLI is a command-line interface to interact with your ElemBio Cloud account data through the ElemBio API. Additionally, the CLI includes helpful tools to download and explore run data.

This guide walks you through installing the CLI, authenticating, and running your first commands.

Install via Homebrew​

Homebrew is a package manager for macOS and Linux that automatically installs and updates command-line tools. If you have Homebrew installed, install the CLI with:

brew tap elembio/tap
brew install elembio

Install via direct download​

If you don't use homebrew, download the binary for your platform, make it executable, and move it onto your PATH. Each URL always points at the latest release.

curl -sSfL https://elembio-cloud-downloads.s3.us-west-2.amazonaws.com/elembio-cli/releases/latest/elembio-darwin-arm64 -o elembio
chmod +x elembio
sudo mv elembio /usr/local/bin/elembio

Confirm the install​

elembio version
elembio help

You should see the following output:

elembio-cli/1.0.0 (60a32841f3870c64b99decd2be5b8cd0fd3833a4; darwin/arm64) go/1.26.3

elembio is a command-line interface for the Element Biosciences Cloud API.

...

Authenticate​

Log in interactively and store credentials under the default profile:

elembio login
# you will be prompted to input an API key
Enter API key: ebp_s6iyTXunEXAMPLE
Successfully authenticated!
  API URL: https://cloud-api.usw2.elembio.io
  Profile: default

Work with runs​

List runs in your organization:

# List runs
elembio runs list
Showing 100 of 2109 total (--max-items 0 for all)
ID                            NAME                 TYPE          STATUS     INSTRUMENT   CREATED
seq_507f1f77bcf86cd799439011  My_Example_Run       sequencing    completed  AV100001     2026-06-04 14:53
seq_6a21f3c4ae4c10fc610d8e92  More_Example_Runs    sequencing    completed  AV100001     2026-06-04 14:53

Get one run by ID or name:

elembio runs get My_Example_Run
elembio runs get seq_507f1f77bcf86cd799439011
# A full run with metrics is returned
Id: seq_507f1f77bcf86cd799439011
Name: My_Example_Run
Description: description of 3_4_2-xsys-A-DL_949769-OBPA-DL for sequencing run on side A_469124
Type: sequencing
...

List files in a run output directory.

elembio runs files My_Example_Run
PATH                           SIZE       MODIFIED
Alignment/R1_L1R05C01S1.aln    11.73 MB   2026-06-04 14:56
AvitiRunStats.json             124.67 KB  2026-06-04 14:58
BaseCalls/I1_C001.zip          3.44 MB    2026-06-04 14:55
...

Download a run output into a local directory:

elembio runs download My_Example_Run --output-dir ./my-run
# The run will begin to download with a progress bar

Downloading run seq_507f1f77bcf86cd799439011
Run: 3_4_2-xsys-A-DL_949769-OBPA-DL
Discovering files... Downloading to ./my-run

[███████░░░░░░░░░░░░░░░░░░] 30.3% 109.14 MB/359.72 MB 28.71 MB/s 21/95 files ETA 9s 28s

See also​

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