Add section: Apptainer

[icaoberg]

🧩 Feature Request: Add Section on Apptainer

Description
Add a new section to the documentation introducing Apptainer — the container platform designed for high-performance computing (HPC) environments.
This section will guide users on how to build, run, and use Apptainer containers on the Lane cluster for reproducible scientific workflows.

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🧭 Suggested Content

• Introduction
  • What Apptainer is and how it differs from Docker or Podman.
  • Benefits for HPC users: portability, reproducibility, and security.
• Installation / Loading
  • How to access Apptainer on the Lane cluster (e.g., module load apptainer).
• Basic Commands
  • Examples of apptainer pull, apptainer build, and apptainer run.
• Running Containers
  • How to execute applications within containers using local images (.sif files) or remote registries.
• Integration
  • How Apptainer integrates with Nextflow, Snakemake, and other workflow engines.
  • Interaction with Conda and Spack environments.
• Best Practices
  • Caching images, managing writable overlays, and working with Lustre or scratch storage.
  • Sharing and versioning containers for collaborative projects.

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🧪 Expected Outcome

A new subsection under Advanced Topics → Apptainer in the documentation.
Users should be able to:

• Run containerized applications efficiently on the Lane cluster.
• Build reproducible and portable HPC workflows.
• Understand the relationship between Apptainer and other tools like Conda and Spack.

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🧰 References

• Apptainer Official Docs
• Apptainer Quick Start Guide
• Using Apptainer on HPC Systems (NERSC)

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✅ Tasks

• Create docs/advanced_topics/apptainer.md
• Add Apptainer section to index.rst
• Include command examples and workflow integration tips
• Cross-link with Conda and Spack sections
• Build and verify documentation locally