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 on the HPC

• Ensure that "$HOME"/dotfiles/install-hpc.sh has been run.
• Switch to the directory in the HPC in which you wish to keep all the repos associated with this project.
• Run git clone https://github.com/SATVILab/Comp_2024_CITEseqHIVE.
• Run cd Comp_2024_CITEseqHIVE
• Run apptainer-pull -o SATVILab
• Run apptainer-vscode
• Within VS Code:
  • In a terminal where the working directory is Comp_2024_CITEseqHIVE, run repos-git-clone.
  • For each analysis/data processing repo (just not this infrastructure repo), e.g. M72_CITEseqHIVE_scRNAseq_Pipeline:
    • Switch to them as your working directory, e.g. cd ../M72_CITEseqHIVE_scRNAseq_Pipeline.
    • Run config-r-renv-restore.
  • In the repo in which you want to work, run radian to start R and then e.g. quarto::quarto_render() to build the quarto project.

How to run within a container on GitHub Codespaces

• Ensure that the GitHub Codespace has access to the following environment variables:
  • GH_TOKEN: Classic PAT for GitHub
• Open GitHub Codespace
• In a terminal where the working directory is Comp_2024_CITEseqHIVE, run repos-git-clone.
• For each analysis/data processing repo (just not this infrastructure repo), e.g. M72_CITEseqHIVE_scRNAseq_Pipeline:
  • Switch to them as your working directory, e.g. cd ../M72_CITEseqHIVE_scRNAseq_Pipeline.
  • Run config-r-renv-restore.
• In the repo in which you want to work, run radian to start R and then e.g. quarto::quarto_render() to build the quarto project.