diff --git a/container/Dockerfile b/container/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..54b8e2a581f7954957e37925b6de2a8baeb4d2fb --- /dev/null +++ b/container/Dockerfile @@ -0,0 +1,30 @@ +from rocker/rstudio:4.1.3 + +RUN apt-get update && \ + apt-get install -y \ + libcurl4-openssl-dev \ + libssl-dev libssh2-1-dev \ + libxml2-dev zlib1g-dev \ + && \ + R -e "install.packages(c('devtools'))" + +# Update the system and install necessary libraries for R packages +RUN apt-get update && apt-get install -y \ + libcurl4-openssl-dev \ + libssl-dev \ + libxml2-dev \ + libxt-dev \ + libgit2-dev \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* + +# Install other R +RUN R -e "install.packages(c('plyr', 'BiocManager'), repos='https://cran.biotools.fr')" \ + && R -e "BiocManager::install(c('snpStats', 'SNPRelate'))" + +# Expose the RStudio Server port +EXPOSE 8787 + +# Start RStudio Server +CMD ["/init"] + diff --git a/container/m2bsgreprod.def b/container/m2bsgreprod.def new file mode 100644 index 0000000000000000000000000000000000000000..cd2c83483d097a570dd784d6816999b63fb6ab9e --- /dev/null +++ b/container/m2bsgreprod.def @@ -0,0 +1,38 @@ +Bootstrap: docker +From: rocker/rstudio:4.1.3 + +%post + # Update the system and install necessary libraries for building R packages + apt-get update && \ + apt-get install -y \ + libcurl4-openssl-dev \ + libssl-dev \ + libssh2-1-dev \ + libxml2-dev \ + libxt-dev \ + libgit2-dev \ + zlib1g-dev \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* + + # Install necessary R packages + R -e "install.packages(c('devtools', 'plyr', 'BiocManager'), repos='https://cran.biotools.fr')" + + # Install Bioconductor packages + R -e "BiocManager::install(c('snpStats', 'SNPRelate'))" + + # Install GenABEL.data from the CRAN archive + R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/GenABEL.data/GenABEL.data_1.0.0.tar.gz', repos=NULL, type='source')" + + # Install the archived GenABEL package from the CRAN archive +R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/GenABEL/GenABEL_1.8-0.tar.gz', repos=NULL, type='source')" + +R -e 'install.packages("genetics")' + +R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/LDheatmap/LDheatmap_1.0-6.tar.gz', repos=NULL, type='source')" + + +%environment + # Set R library paths if necessary + export R_LIBS_USER=/usr/local/lib/R/site-library +