CCBR How-Tos
Home
Contributors
Containers
Using containers as development environments
Datashare
LucidChart
Snakemake
Zenodo
Conda Mamba
Using the shared CCBR mamba installation on Biowulf
Move from Conda to Mamba
Containers
Build docker containers interactively with Google Cloud Shell
How to use containers with singularity on biowulf
Using containers as development environments
Using containers as development environments
GitHub
GitHub Actions demo
Guide
Overview of GitHub Topics
GitHub Setup: Preparing the Environment
GitHub HowTo: Basic Commands
GitHub Basics: Repository
GitHub Basics: Documentation
GitHub Basics: GitHub Actions
GitHub HowTo: Pre-Commit
GitHub Best Practices: Projects and Pipelines
GitHub Best Practices: TechDev projects
Authentication with GitHub
Connect to GitHub with SSH keys
Tokens
Classic Personal Access Tokens
Fine-Grained Personal Access Tokens
HPCDME
HPCDME Setup
File Transfers from Biowulf
File Transfer from HELIX
Code Club
2025 02 11 Journal Club
Improving bioinformatics software quality through teamwork
2025 08 26 Establishing Code Club
Establishing a Community of Practice
Generative AI tools
GitHub Copilot CLI
Set up CCBR Superpowers skills
GitHub Copilot in VS Code
Reproducible AI Practices for Bioinformatics
Maintenance
How to Release New Versions
R Package
Create from Conda
setup
Creating the package
common issues
Shiny
Publishing Shiny Apps on NCI’s POSIT Connect Servers
Developing Shiny Apps
Publishing Shiny Apps to the Development Server
Publishing Shiny Apps to the Production Servers
UCSC
Overview
Generating Inputs
Generating Track information
Generating New Tracks
Containers
Using containers as development environments
Using containers as development environments
Author
Kelly Sovacool
Note
Presented in CCBR Code Club on Oct 07, 2026:
Presentation slides
Recording coming soon!
How to use containers with singularity on biowulf
Using containers as development environments