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Merge branch 'trs/mention-singularity-more'
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tsibley committed Jan 31, 2024
2 parents 3d845bd + ec0bec4 commit ec3ff3c
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4 changes: 2 additions & 2 deletions doc/commands/build.rst
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Expand Up @@ -22,8 +22,8 @@ The build directory should contain a Snakefile, which will be run with
snakemake.

You need at least one runtime available to run a build. You can test if the
Docker, Conda, ambient, or AWS Batch runtimes are properly supported on your
computer by running::
Docker, Conda, Singularity, ambient, or AWS Batch runtimes are properly
supported on your computer by running::

nextstrain check-setup

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3 changes: 2 additions & 1 deletion doc/commands/index.rst
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Expand Up @@ -21,7 +21,8 @@ Nextstrain command-line interface (CLI)

The `nextstrain` program and its subcommands aim to provide a consistent way to
run and visualize pathogen builds and access Nextstrain components like Augur
and Auspice across computing platforms such as Docker, Conda, and AWS Batch.
and Auspice across computing platforms such as Docker, Conda, Singularity, and
AWS Batch.

Run `nextstrain <command> --help` for usage information about each command.
See <:doc:`/index`> for more documentation.
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2 changes: 1 addition & 1 deletion doc/glossary.rst
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Expand Up @@ -20,7 +20,7 @@ documentation.

computing platform
The foundation of a :term:`computing environment` (or part of it), such
as Docker, Conda, AWS Batch, etc.
as Docker, Conda, Singularity, AWS Batch, etc.

runner
The code (i.e. Python module, e.g. :file:`nextstrain/cli/runner/docker.py`)
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3 changes: 2 additions & 1 deletion nextstrain/cli/__init__.py
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Expand Up @@ -3,7 +3,8 @@
The `nextstrain` program and its subcommands aim to provide a consistent way to
run and visualize pathogen builds and access Nextstrain components like Augur
and Auspice across computing platforms such as Docker, Conda, and AWS Batch.
and Auspice across computing platforms such as Docker, Conda, Singularity, and
AWS Batch.
Run `nextstrain <command> --help` for usage information about each command.
See <:doc:`/index`> for more documentation.
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4 changes: 2 additions & 2 deletions nextstrain/cli/command/build.py
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Expand Up @@ -5,8 +5,8 @@
snakemake.
You need at least one runtime available to run a build. You can test if the
Docker, Conda, ambient, or AWS Batch runtimes are properly supported on your
computer by running::
Docker, Conda, Singularity, ambient, or AWS Batch runtimes are properly
supported on your computer by running::
nextstrain check-setup
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