Dockerfile

# Dockerfile

# Use R 3.5.1 as a base image
#FROM docker.repository.cloudera.com/cdsw/engine:8
FROM rocker/rstudio-stable:3.5.1
#RUN rm /etc/apt/sources.list.d/*

# install java develop kit and rJava
RUN apt-get update && \
    apt-get install -y default-jdk
RUN R CMD javareconf
RUN R -e "install.packages('rJava', dependencies = TRUE)"

# install devtools
RUN apt-get update
RUN apt-get install -y \
    build-essential \
    libcurl4-gnutls-dev \
    libxml2-dev \
    libssl-dev \
    libgit2-dev \
# install other
    libfontconfig1-dev \
    libcairo2-dev \
    libharfbuzz-dev \
    libfribidi-dev \
    libfreetype6-dev \
    libpng-dev \
    libtiff5-dev \
    libjpeg-dev \
    libboost-dev

# install devtools
RUN apt-get update
RUN apt-get install -y \
    build-essential \
    libcurl4-gnutls-dev \
    libxml2-dev \
    libssl-dev \
    libgit2-dev \
    # install other
    libfontconfig1-dev \
    libcairo2-dev
#ADD pkgs /home/rstudio/pkgs

# Install OHDSI packages manually
RUN R -e "install.packages('BH'); install.packages('/home/rstudio/pkgs/RcppEigen_0.3.3.7.0.tar.gz', repos = NULL, type = 'source'); install.packages('/home/rstudio/pkgs/openxlsx_4.1.0.tar.gz', repos = NULL, type = 'source'); install.packages('/home/rstudio/pkgs/latticeExtra_0.6-28.tar.gz', repos = NULL, type = 'source'); install.packages('rms'); install.packages('Hmisc'); devtools::install('./Andromeda', upgrade = 'never'); devtools::install('./DatabaseConnector', upgrade = 'never'); devtools::install('./ParallelLogger', upgrade = 'never'); devtools::install('./FeatureExtraction', upgrade = 'never'); devtools::install('./Cyclops', upgrade = 'never'); devtools::install('./EmpiricalCalibration', upgrade = 'never'); devtools::install('./MethodEvaluation', upgrade = 'never');  devtools::install('./OhdsiRtools', upgrade = 'never'); devtools::install('./OhdsiSharing', upgrade = 'never'); devtools::install('ROhdsiWebApi', upgrade = 'never'); devtools::install('./CohortMethod', upgrade = 'never'); devtools::build('./CohortDiagnostics'); install.packages('/home/rstudio/pkgs/CohortDiagnostics_2.0.0.tar.gz', repos = NULL, type = 'source'); install.packages('/home/rstudio/pkgs/PatientLevelPrediction_5.0.5.tar.gz', repos = NULL, type = 'source')"

# PLP conda env settings
RUN R -e "reticulate::install_miniconda(force = TRUE); PatientLevelPrediction::configurePython(envname='r-reticulate', envtype = 'conda'); install.packages('Keras'); Keras::install_keras(method = 'conda'); reticulate::conda_install(envname='r-reticulate', packages = c('scikit-survival'), forge = T, pip = T); reticulate::conda_install(envname='r-reticulate', packages = c('pytorch', 'torchvision', 'cpuonly'), forge = TRUE, pip = FALSE, channel = 'pytorch', pip_ignore_installed = TRUE, conda = 'auto')"

# install JDBC driver for Oracle
RUN R -e "DatabaseConnector::downloadJdbcDrivers(dbms = 'oracle',pathToDriver = '/home/rstudio/jdbc')"