README

The purpose of this compendium is to [briefly describe the compendium's goals and objectives]

Contact

For more information, please contact:

• [Name], [Email Address]
• [Name], [Email Address]

Links

• [URLs to data sources (e.g. OneDrive), GitHub repos, publications, etc.]

Details

How to run within a container in a Linux environment automatically

Details

How to run a project "automatically" in a container on a "fresh" Linux system using apptainer

• Store raw data in a folder whose path is specified in ~/.Renviron as PATH_RAW_DATA (absolute path).
  • Note: not for us.
• Clone analysis repo:
  • Run git clone https://github.com/SATVILab/CompTASAAuto.
  • Run cd CompTASAAuto
• Get apptainer image from GitHub Container Registry:
  • Run mkdir -p /scratch/$USER/.cache/apptainer
  • Run apptainer build --force /scratch/$USER/.cache/apptainer/comptasaauto.sif docker://ghcr.io/SATVILab/CompTASAAuto:latest
• Run analysis:
  • apptainer exec /scratch/$USER/.cache/apptainer/comptasaauto.sif ./scripts/run_analysis.sh

Or, alternatively, run scripts/run_setup_and_analysis.sh.