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FilTar Development Container

This directory contains the development container configuration for the FilTar project. The devcontainer provides a consistent development environment that can be easily spun up in GitHub Codespaces, VS Code Remote Containers, or other devcontainer-compatible tools.

Features

Essential Requirements ✓

  • Conda Environment: Pre-configured with conda for package management
  • Snakemake 8: Snakemake 8.30.0 installed for workflow management

Desired Requirements ✓

  • R Support: R development environment with syntax highlighting and debugging extensions
  • Snakemake Extensions: Syntax highlighting and language support for Snakemake workflows
  • GitHub Integration: GitHub Actions and Pull Request extensions for seamless GitHub workflow
  • Python Support: Full Python development environment with linting and debugging capabilities

Usage

GitHub Codespaces

  1. Open the repository in GitHub
  2. Click the "Code" button and select "Codespaces"
  3. Click "Create codespace on main" (or your preferred branch)
  4. Wait for the container to build and the environment to be set up

VS Code Remote Containers

  1. Install the "Remote - Containers" extension in VS Code
  2. Open the repository in VS Code
  3. Press Ctrl+Shift+P (or Cmd+Shift+P on Mac) and select "Remote-Containers: Reopen in Container"
  4. Wait for the container to build and the environment to be set up

Environment Setup

The container automatically:

  1. Uses the Rocker R 4.2 base image with R pre-installed
  2. Installs essential R packages (remotes, testthat, languageserver) via devcontainer features
  3. Creates a conda environment named test-environment from environment.yml
  4. Installs Snakemake 8.30.0 and Python 3.12
  5. Installs the FilTar R package from GitHub
  6. Configures VS Code with appropriate extensions for R, Python, Snakemake, and GitHub workflows

Activating the Environment

The conda environment test-environment is automatically activated when you open a new terminal. If you need to manually activate it, use:

conda activate test-environment

Included Extensions

  • Python: ms-python.python, ms-python.pylint, ms-python.flake8, ms-python.autopep8
  • R: reditorsupport.r, rdebugger.r-debugger, posit.air-vscode
  • Snakemake: snakemake-lang.snakemake-lang, tfehlmann.snakefmt
  • GitHub: github.vscode-github-actions, github.vscode-pull-request-github
  • Additional: JSON, YAML support

Troubleshooting

Common Issues and Solutions

R Terminal Issues: If R terminals cannot attach, the devcontainer automatically configures r.rterm.linux and r.rpath.linux to point to the R installation provided by the Rocker base image.

Python Interpreter Issues: The devcontainer creates workspace-specific settings to ensure the correct Python interpreter from the conda environment is used. If VS Code doesn't detect it automatically, check the bottom-left status bar and select the correct interpreter.

GitHub Extension Issues: If GitHub-related extensions show commit errors during initial setup, these typically resolve once the environment is fully built and VS Code restarts.

Manual Troubleshooting Steps

If you encounter issues with the environment setup:

  1. Check the terminal output during container creation
  2. Manually run the setup script: bash .devcontainer/setup.sh
  3. Verify the conda environment: conda env list
  4. Check Snakemake installation: snakemake --version
  5. Verify R installation: R --version
  6. Check Python interpreter: look for /opt/conda/envs/test-environment/bin/python in VS Code status bar