---
name: singularity-container-manager
description: Singularity container management skill for HPC-compatible containerized execution
allowed-tools:
  - Read
  - Write
  - Glob
  - Grep
  - Edit
  - WebFetch
  - WebSearch
  - Bash
metadata:
  version: "1.0"
  category: bioinformatics
  tags:
    - infrastructure
    - containers
    - singularity
    - hpc
---

# Singularity Container Manager Skill

## Purpose
Provide Singularity container management for HPC-compatible containerized execution.

## Capabilities
- Container building from recipes
- Registry pull and caching
- Bind mount configuration
- GPU passthrough
- MPI integration
- Security compliance for HPC

## Usage Guidelines
- Build containers from definition files
- Cache containers for repeated use
- Configure bind mounts appropriately
- Enable GPU for accelerated workloads
- Integrate with MPI for parallel computing
- Ensure HPC security compliance

## Dependencies
- Singularity/Apptainer
- Docker
- BioContainers

## Process Integration
- Reproducible Research Workflow (reproducible-research)
- All analysis pipelines