generated: '2026-08-04'
method: searched
source: https://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities
docs: https://documentation.dnanexus.com/getting-started/cli-quickstart
downloads: https://documentation.dnanexus.com/downloads
name: dx
description: >-
  dx is the DNAnexus Platform command-line client, shipped inside the dx-toolkit
  (DNAnexus Platform SDK) alongside the dxpy Python bindings. It is a thin, complete
  front end over the Platform API: every dx subcommand maps onto one or more API
  methods, and `dx api` will invoke any API method directly.
source_repo: https://github.com/dnanexus/dx-toolkit
license_repo: https://github.com/dnanexus/dx-toolkit/blob/master/COPYING
install:
- method: pip
  command: python3 -m pip install dxpy
  note: installs both the dx CLI and the Python SDK
- method: source
  command: python3 -m pip install -e dx-toolkit/src/python
  note: recommended local/development install
command_groups:
- group: Get started
  commands: [dx, help]
- group: Manage your login session
  commands: [login, logout, exit, whoami, env, clearenv, setenv]
- group: Navigate and organize files
  commands: [ls, tree, pwd, select, cd, cp, mv, mkdir, rmdir, rm, rmproject, archive,
    unarchive, list database files]
- group: View, download, and upload data
  subgroups: [File transfer, View data, Create data objects, Data object operations,
    Searching, Project management, Datasets and cohorts]
- group: Manage metadata
  commands: [set_details, get_details, set_visibility, add_types, remove_types, tag,
    untag, rename, set_properties, unset_properties]
- group: Build and modify workflows
  commands: [add stage, remove stage, update stage, update workflow, list stages]
- group: Run and manage apps
  subgroups: [Build and publish, Manage app access, Run and monitor, Search for executables
      and executions, Batch operations]
- group: Manage organizations
  subgroups: [Organization setup, Manage members, Searching]
- group: Share projects and data
  commands: [invite, uninvite]
- group: Additional tools
  commands: [api, build_asset, upgrade]
utilities:
- name: dx-app-wizard
  purpose: scaffold a new app(let)
- name: dx-fetch-bundled-depends
  purpose: fetch an app's bundled dependencies
- name: dx-generate-dxapp
  purpose: generate a dxapp.json app metadata file
- name: dx-jobutil-add-output
  purpose: add a value to a job's output from inside the execution environment
- name: dx-jobutil-dxlink
  purpose: emit a DNAnexus link for a data object
- name: dx-jobutil-new-job
  purpose: launch a subjob from inside a running job
- name: dx-jobutil-parse-link
  purpose: parse a DNAnexus link
- name: dx-jobutil-report-error
  purpose: report an AppError/AppInternalError from inside a job
- name: dx-jobutil-get-identity-token
  purpose: request a job identity token (OIDC) for access to external cloud services
key_flows:
- name: Log in and select a project
  commands: [dx login, dx select, dx pwd]
- name: Upload and describe data
  commands: [dx upload, dx describe, dx ls]
- name: Build and run an app
  commands: [dx-app-wizard, dx build, dx run, dx watch]
- name: Search the platform
  commands: [dx find data, dx find executions, dx find apps, dx find projects]
- name: Call any API method directly
  commands: [dx api]
  note: '`dx api <class-id> <method> <input JSON>` invokes any of the ~206 documented
    Platform API methods without a binding.'
related_binaries:
- name: Upload Agent (ua)
  docs: https://documentation.dnanexus.com/user/objects/uploading-and-downloading-files/batch/upload-agent
- name: Download Agent (dxda)
  url: https://github.com/dnanexus/dxda
- name: dxfuse
  url: https://github.com/dnanexus/dxfuse
- name: dxCompiler
  url: https://github.com/dnanexus/dxCompiler
x-evidence:
  fetched: '2026-08-04'
  url: https://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities.md
  http_status: 200