Docker container for Bioconductor 3.17 version

Hei,

As this might be of interest, on this link below you can find the docker container I use to run the CAGEr 2.6.1 version

https://hub.docker.com/r/cbgr/cager261

The dockerfile is as below:

# Docker install R 4.3, Bioconductor 3.17
FROM bioconductor/bioconductor_docker:3.17

# Set up folder structure
WORKDIR /opt/software

# Install CAGEr 2.6.1
RUN R -e 'BiocManager::install("CAGEr")'

# Install other R dependencies
COPY requirements.R /opt/software/requirements.R
RUN Rscript requirements.R
ENV R_LIBS=${R_LIBS}:/opt/software

The requirements.R file is as below:

#################################
## List of R packages required ##
#################################
.libPaths( c( "/opt/software" , .libPaths() ) )

## CRAN packages:
required_packages_cran = c(
  "optparse",         ## Read in data
  "rlang",            ## Error handling
  "tidyr",            ## Data formatting and manipulation
  "viridis",          ## Plotting
  "ggplot2",          ## Plotting
  "gplots")           ## Plotting

message("; Installing these R packages from CRAN repository: ", required_packages_cran)
install.packages(required_packages_cran, repos="https://cran.uib.no/", lib="/opt/software")

## Bioconductor packages:
required_packages_bioconductor <- c(
  "BSgenome.Hsapiens.UCSC.hg38",
  "ChIPseeker",
  "TxDb.Hsapiens.UCSC.hg38.knownGene",
  "org.Hs.eg.db",
  "rtracklayer")

message("; Installing these R Bioconductor packages: ", required_packages_bioconductor)
BiocManager::install(required_packages_bioconductor, lib="/opt/software")

charles-plessy / CAGEr

Docker container for Bioconductor 3.17 version #104