Runtimes

Nextstrain’s runtimes are specific computing environments in which Nextstrain CLI expects to find and run other Nextstrain programs, like Augur and Auspice. In turn, Nextstrain CLI provides a consistent set of commands to run and visualize Nextstrain pathogen builds regardless of the underlying runtime in use. Together, this allows Nextstrain to be used across many different computing platforms and operating systems.

The nextstrain build, nextstrain view, and nextstrain shell commands all require a runtime, as they require access to other Nextstrain software.

The nextstrain setup, nextstrain check-setup, and nextstrain update commands manage the runtimes available for use by the commands above. The nextstrain version command’s --verbose option reports detailed version information about all available runtimes.

Other Nextstrain CLI commands, such as the nextstrain remote family of commands and the related nextstrain login and nextstrain logout commands, do not require a runtime. They may be used without any prior set up of a runtime.

The runtimes currently available are the:

Runtimes are managed (maintained, tested, versioned, released) by the Nextstrain team, except for the ambient runtime. The ambient runtime is special in that it’s whatever computing environment in which Nextstrain CLI itself is running (that is, it’s managed by the user).

You can set up and use multiple runtimes on the same computer, for example if you want to use them in different contexts. Runtime-using commands let you select a different runtime than your default with command-line options (e.g. --docker, --conda, and so on). For example, you might use the Docker runtime to run small builds locally and then use the AWS Batch runtime to run large scale builds with more computing power.

If you pick one runtime and later realize you want to switch, you can go back and set up the other.

Comparison

Isolation level

Containerized?

Locality

External dependencies

Docker runtime

great (3)

yes

local or remote

docker command

Conda runtime

some (1)

no

local

none

Singularity runtime

good (2)

yes

local

singularity command

Ambient runtime

none (0)

no

local

many

AWS Batch runtime

great (3)

yes

remote

AWS account with Batch set up

Isolation level

A relative ranking from least isolated (none, 0) to most isolated (great, 3) from the underlying computer system.

Containerized?

A containerized computing platform provides a higher degree of isolation, which in turn usually means a higher degree of portabililty and reproducibility across different computers and users.

Locality

Local means “on the same computer where nextstrain is being run”. Remote means “on a different computer”.

Docker is most often used to run containers locally, but can also be used to run them remotely.

External dependencies

Third-party programs or configuration which are required to use a runtime but not managed by nextstrain setup and nextstrain update.

Compatibility

Switching runtimes or updating the version of a runtime may result in different versions of Nextstrain components like Augur and Auspice as well as other programs, and thus different behaviour. Use the nextstrain version command’s --verbose option to report detailed version information about all available runtimes.

Exact behavioural compatibility is not guaranteed between different runtimes (e.g. between the Docker vs. Conda runtimes) or between versions of the same runtime (e.g. between Docker runtime images nextstrain/base:build-20230714T205715Z and nextstrain/base:build-20230720T001758Z). However, the containerized runtimes (Docker, Singularity, AWS Batch; see comparison above) will usually have identical behaviour given the same runtime version (e.g. build-…) as they are all based the same runtime image (nextstrain/base). Any variance is typically due to use of external resources (intentional or otherwise) from outside the container.