Welcome to BioAnalyze HPC

Overview:

• BioAnalyze HPC
  • System at a Glance
  • Helper Libraries
  • Getting Started
  • Show Case
  • Deploy all the Bioinformatics Related Things!

Getting Started:

• Access
  • SSH Access
  • JupyterHub Access
• Onboarding Tutorials
  • Configuration
  • Jupyterhub Access
  • Getting an Instance
  • Get to Know Your System
  • File Systems
  • BioAnalyze HPC Helper Libraries
  • Additional Information
• Best Practices
  • Start Small and Save Money
  • Submit Larger jobs to the Scheduler
  • Exceptions

Software:

• Software Organization Overview
• Install Software with Conda
  • Default conda configuration
• Register your Software to Jupyter
  • Python
  • R
  • Custom R with RStudio
• Spack Package Manager
  • Basic Usage
• Spack Example - Gromacs
  • Gromacs + GPU
  • Gromacs + Other Variant Combinations

Workflow Mangers:

• Prefect
  • Prefect Local Dask Cluster - Example
  • Prefect Dask Gateway Cluster - Example
• Nextflow
  • Nextflow with SLURM Tutorial

Web Applications:

• Proxy Web Apps
  • Proxy URLs
  • Starting and Proxying Processes
  • Accessing Arbitrary Ports
  • More Examples
  • Gotchas
  • Example - ExCellxGene
  • Launch the ExCellxGene Web App
• ContainDS
  • RShiny
  • Dash
  • Flask
  • Flask
  • Streamlit

Consulting:

• Contributing
  • Bootstrap
  • Serve Locally
• Contact

Indices and tables

• Index

• Module Index

• Search Page