Hint
This is reference documentation for the Nextstrain CLI (command-line interface). If you're just getting started with Nextstrain, please see :doc:`our general documentation <docs:index>` instead.
The Nextstrain CLI is a program called nextstrain. It aims to provide a
consistent way to run and visualize pathogen builds and access Nextstrain
components like :doc:`Augur <augur:index>` and :doc:`Auspice <auspice:index>`
computing platforms, such as
:doc:`/runtimes/docker`,
:doc:`/runtimes/conda`,
:doc:`/runtimes/singularity`, and
:doc:`/runtimes/aws-batch`.
Note
If you're unfamiliar with Nextstrain builds, you may want to follow our :doc:`docs:tutorials/running-a-workflow` tutorial first and then come back here.
.. toctree::
:maxdepth: 3
Introduction <self>
installation
upgrading
AWS Batch <aws-batch>
.. toctree::
:caption: Commands
:name: commands
:titlesonly:
:maxdepth: 3
commands/build
commands/view
commands/deploy
commands/remote/index
commands/remote/list
commands/remote/download
commands/remote/upload
commands/remote/delete
commands/shell
commands/update
commands/setup
commands/check-setup
commands/login
commands/logout
commands/whoami
commands/authorization
commands/version
.. toctree::
:caption: Remotes
:titlesonly:
nextstrain.org <remotes/nextstrain.org>
Amazon S3 <remotes/s3>
.. toctree::
:caption: Runtimes
:titlesonly:
Overview <runtimes/index>
Docker <runtimes/docker>
Conda <runtimes/conda>
Singularity <runtimes/singularity>
AWS Batch <runtimes/aws-batch>
Ambient <runtimes/ambient>
.. toctree::
:caption: Configuration
:titlesonly:
Config file <config/file>
Paths <config/paths>
.. toctree::
:caption: Development
:titlesonly:
glossary
The Nextstrain CLI glues together many different components. Below is a brief overview of the big picture:
