From 0961b9eb3564f7f776c1791c8a27e3e5e5f29567 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Wed, 31 Jan 2024 10:22:56 -0800 Subject: [PATCH] Add instructions for singularity runtime Descriptive snippet copied from Nextstrain CLI docs. --- src/install.rst | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/src/install.rst b/src/install.rst index 1d5107ab..a64f27d5 100644 --- a/src/install.rst +++ b/src/install.rst @@ -184,6 +184,29 @@ Set up a Nextstrain runtime .. include:: snippets/nextstrain-setup-conda.rst + .. group-tab:: Singularity (Apptainer) + + Singularity is a container system freely-available for Linux platforms. It is commonly available on institutional HPC systems as an alternative to Docker, which is often not supported on such systems. + + The Singularity project forked into two separate projects in late 2021: `SingularityCE `__ and `Apptainer `__. Either fork should work with Nextstrain CLI, as both projects still provide very similar interfaces and functionality via the ``singularity`` command. + + .. note:: + + These instructions are for institutional HPC systems that have Singularity installed and configured. You may need to load it with ``module load singularity``. If you don't have Singularity available, consider using one of the other runtimes or continue by installing `SingularityCE `__/`Apptainer `__. + + 1. Check that Singularity is available in your environment. + + .. code-block:: bash + + singularity --version + + 2. Set up the runtime: + + .. code-block:: none + + nextstrain setup --set-default singularity + + .. group-tab:: Ambient (advanced) .. We use the phrase "custom Conda environment" to refer to a Conda environment managed by the user for use with the ambient runtime.