diff --git a/docker-bsseq/Dockerfile b/docker-bsseq/Dockerfile new file mode 100644 index 0000000..9a686c7 --- /dev/null +++ b/docker-bsseq/Dockerfile @@ -0,0 +1,37 @@ +# Use the Rocker R image +FROM rocker/r-ver:4.4.0 + +# Copy installBioc.r script +RUN cp /usr/local/lib/R/site-library/littler/examples/installBioc.r /usr/local/bin/installBioc.r + +# Install BiocManager +RUN Rscript -e "install.packages('BiocManager')" + +# Install system dependencies +RUN apt-get update && apt-get -y install \ + less \ + curl \ + gzip \ + lsof \ + libz-dev \ + libbz2-dev \ + liblzma-dev \ + libxml2 \ + libxml2-dev \ + libxt6 \ + libglpk-dev \ + libmysqlclient21 \ + libcurl4-openssl-dev && \ + python3 \ + python3-pip && \ + apt-get clean + +# Install Bioconductor packages +RUN R -e "install.packages('BiocManager'); BiocManager::install(version = '3.19')" + +# Install required R and Bioconductor packages +RUN R -e "install.packages(c('argparse', 'data.table')); \ + BiocManager::install(c('HDF5Array', 'bsseq', 'DSS', 'GenomicRanges', 'IRanges'))" + +# Entry point for the container +CMD ["bash"] \ No newline at end of file