Guide to Guthridge/James lab compute resources

Contents:

• Basic Unix
  • Streams
    • The Pipe
  • Unix commands
• Local data sources
  • Cluster
  • ADI
  • o3
• Online data sources
  • Google cloud
• Extant datasets
• Cloud computing resources
  • Virtual machines
• Jupyter
  • Using Jupyter notebooks on Walnut
• slurm
  • srun
  • sbatch
• Local computing resources
  • Walnut
    • ssh
    • ssh-key
  • Software
    • Modules
    • Conda
    • vscode
  • Folders
    • Home
    • Share
    • Scratch
    • Shared References
    • Object Storage
• Processing Novaseq Runs
  • Demultiplexing
    • SampleSheet
    • Running bcl2fastq
  • Alignment
    • Snakemake
  • Directory structure
• Processing 10X Genomics scRNA-seq Runs
  • Demultiplexing (BCL -> FASTQ)
    • Sample Sheet
    • bcl-convert
    • Cellranger mkfastq
  • Monitoring the pipeline
• Accessing Public Datasets
• Git
  • Setting up to use Gitlab
• Rclone
  • Quickstart
  • Setup
    • Installation
    • Configuration
    • Using without a config file
  • Useful Parameters
• RStudio
  • Using RStudio on Walnut
    • Pre-written RStudio job script
• Containerization
  • Docker
  • Singularity