generated: '2026-07-20'
method: searched
source: https://developer.onecodex.com/api-reference/command-line-interface.md ; https://github.com/onecodex/onecodex
name: onecodex
binary: onecodex
repo: https://github.com/onecodex/onecodex
license: MIT
install:
  - pip install onecodex
  - pip install 'onecodex[all]'   # + Jupyter/IPython notebook extensions
requires: Python 3.10+
authentication:
  - onecodex login   # interactive; stores API key
  - env var ONE_CODEX_API_KEY
commands:
  - group: login / logout
    purpose: Authenticate the CLI via API key or username/password.
  - group: upload
    purpose: Upload FASTA/FASTQ sequence files as Samples (with multipart support).
  - group: samples
    purpose: List, retrieve, and manage samples.
  - group: analyses / classifications / panels
    purpose: Retrieve analysis results (classifications, panels, alignments).
  - group: documents
    purpose: Upload and manage arbitrary documents.
  - group: scripts
    purpose: Run custom bioinformatics workflows/jobs from the command line.
notebook_extension: >-
  The [all] extra adds One Codex integration for IPython/Jupyter interactive analysis
  and data visualization.