🐳 𝓡 Custom Tidyverse Docker Image

• Installed Dependencies
• Build the Image
• Changelog

My development tidyverse image is based on r-base.

Installed Dependencies

It adds:

• radian as R console replacement
• shiny server
  • You can start a shiny server using shiny-server.sh
  • For details, check the rocker/shiny repo
• visidata for the rvisidata package
• A whole bunch of libraries for a number of different R packages, mostly for bioinformatics analyses

Build the Image

Run the building process manually using the following code (adapting the version).

docker login
docker build --no-cache -t mytidyverse .
docker tag mytidyverse paulklemm/mytidyverse:4.3.1-3
docker push paulklemm/mytidyverse:4.3.1-3

You can also use the makefile.

make VERSION=4.3.1-3

Or adapt the default VERSION in the makefile and run make.

Changelog

• 2024-10-08
  • Add singularity
• 2024-10-01
  • Add keychain
• 2024-09-30
  • Add ZSH
• 2024-09-27
  • Add Quarto
  • Bump to 4.4.1
• 2024-05-14
  • Bump to 4.4.0
  • Add Jupyter Notebook
• 2023-09-15
  • Add igraph dependency for scvi
• 2023-09-11
  • Add potential fix for scvi by reverting to pandas < 2.0.0
• 2023-09-06
  • Bump to 4.3.1
  • Add scvi tools to interface HypoMap packages
• 2022-08-03
  • Add libgeos-dev dependency required for Seurat
• 2022-08-02
  • Add libncurses5 to comply with Lukas' fibeR package
  • Bump to 4.2.1
• 2022-02-25
  • Add anndata and scanpy python modules
  • Bump to 4.1.2
• 2021-09-03
  • Fix requirements for magick and tesseract package
• 2021-08-16
  • Add some library to allow ggstatsplot to be installed and bump to 4.1.1
• 2021-05-26
  • Switch to rocker/r-ver as all rocker images >= 4.0.0 are now on Ubuntu 20.04 instead of Debian
• 2021-02-25
  • Bump to 4.0.4
• 2020-11-30
  • Add jags and ibmagick++-dev
• 2020-10-20
  • Clean up Dockerfile and bump to 4.0.3
• 2020-09-09
  • Add required libraries for TFBSTools package
• 2020-08-27
  • Remove RStudio Server
  • Switch to rocker/r-ubuntu:20.04
• 2020-08-25
  • Add RStudio Server
• 2020-07-21
  • Bump to r-base:4.0.2
• 2020-04-17
  • Add tmux for rvisidata
• 2020-04-09
  • Bump to r-base:3.6.3
  • Remove all R packages
  • Add standard shiny installation
• 2020-02-18
  • Bump to r-base:3.6.2
  • Add renv
  • Add drake
• 2020-01-13
  • Add tidlog
• 2019-12-13
  • Add Visidata not installed properly #4
• 2019-12-12
  • Add hack for fixing issue Fix GenomicAlignments error #3
• 2019-11-05
  • Add visidata 2 pre-release
  • Add Fix GenomicAlignments error #3
• 2019-10-28
  • Add styler, knitr, rmarkdown and vroom
• 2019-10-17
  • Add DESeq2
• 2019-09-02
  • Fix broken Uni-Muenster CRAN link
  • Update default variables to point to r-base 3.6.1
• 2019-04-10
  • Radix package was renamed to distill
• 2019-04-05
  • Bump base image to r-base:3.5.3
  • Add makefile
• 2019-01-29
  • Add Seurat package for Single Cell RNA-Seq analysis
  • rtichoke was renamed to radian
• 2019-01-07
  • Switch to r-base:3.5.2 as base image