Devcontainer: use prebuilt GHCR image + conda/mamba Bioconductor env for fast Codespaces (R 4.3) #57
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added 25 commits
September 18, 2025 10:00
… env in case of a restart
…1.81.0-1, ggplot2 4.0.0, ggtree 3.99.0, and ggiraph 0.9.1
…sea and the proper ubuntu libraries necessary to install qsea
… install GenomeInfoDb and other packages necessary for qsea
…d a package list generator script
…devcontainer without conflicts
… specify workspaceFolder and check that remotes package is install before executing remotes::install_local
…reated the env with --override-channels, and switched the shell into shiny_env before CRAN/GitHub installs
…ward 3838, keep postCreate install
… R to PATH, install languageserver/imsig/immunedeconv, create vscode user, clean caches
…age and remoteUser=vscode
…ATH, install languageserver/imsig/immunedeconv, add vscode user
Collaborator
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We don't want to target ggplot2 v3, we want the package to work on v4 |
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added 2 commits
October 8, 2025 15:22
…t.{slim,full}; install devtools helpers; put mesa_env on PATH; install remotes/languageserver/imsig/immunedeconv
… mesa_env R; set plot size; keep postCreate install
…; tag latest -> codespaces-slim; enable registry cache
SPPearce
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Nov 10, 2025
…f not having Anaconda's paid license
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added 4 commits
November 18, 2025 11:14
- Drop unused package_list.txt/generate_package_list.R from workflow paths - Rebuild images on codespace_env_implementation, dev, and main
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SPPearce
approved these changes
Nov 19, 2025
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This PR improves the dev environment to deliver fast, reproducible Codespaces by pulling a prebuilt GHCR image and standardizing on a conda/mamba-based R/Bioconductor stack.
This includes:
• Devcontainer
○ Use prebuilt image: ghcr.io//mesa/devcontainer:codespace_env_implementation
○ Run as non-root vscode user
○ Keep postCreateCommand to install the local package
• Dockerfile (image build)
○ Base: miniconda3 with mamba
○ Create mesa_env from package_list.txt
○ Only conda-forge + bioconda, strict priority, --override-channels
○ Add env to PATH so R is available without activation
○ Preinstall: languageserver, imsig, omnideconv/immunedeconv
○ Create vscode user; clean conda/mamba caches
• Deps generation
○ generate_package_list.R: map Bioconductor/CRAN properly, drop base R stdlib
○ Correct mappings (e.g., limma/plyranges → bioconductor-, workflows → r-)
○ Target R 4.3 (with ggplot2<4)
• CI
○ Workflow builds & pushes the image for this branch/tag
• Cleanup
○ Removed old Dockerfiles to avoid conflicts
○ Added verbose mamba where useful for debugging