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Update HADES Dockerfile #32

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Update HADES Dockerfile #32

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ee14661
Update to rocker/rstudio:4.2.3 - fixes #31
anthonysena Feb 26, 2024
e188551
Download all JDBC drivers - fixes #19
anthonysena Feb 26, 2024
8f0318b
Change install2.r calls to specify the Posit package manager to ensur…
anthonysena Feb 26, 2024
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41 changes: 17 additions & 24 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
# syntax=docker/dockerfile:1
FROM rocker/rstudio:4.2.1
MAINTAINER Lee Evans <[email protected]>
FROM rocker/rstudio:4.2.3
LABEL Lee Evans <[email protected]>

# install OS dependencies including java and python 3
RUN apt-get update && apt-get install -y openjdk-11-jdk liblzma-dev libbz2-dev libncurses5-dev curl python3-dev python3.venv \
&& R CMD javareconf \
&& rm -rf /var/lib/apt/lists/*

# install utility R packages
RUN install2.r \
RUN install2.r --error --skipinstalled --repos "https://packagemanager.posit.co/cran/latest" \
openssl \
httr \
xml2 \
Expand All @@ -23,9 +23,9 @@ RUN --mount=type=secret,id=build_github_pat \
&& cp /tmp/Renviron /usr/local/lib/R/etc/Renviron

# install useful R libraries to help RStudio users to create/use their own GitHub Personal Access Token
RUN install2.r \
usethis \
gitcreds \
RUN install2.r --error --skipinstalled --repos "https://packagemanager.posit.co/cran/latest" \
usethis \
gitcreds \
&& rm -rf /tmp/download_packages/ /tmp/*.rds

# create Python virtual environment used by the OHDSI PatientLevelPrediction R package
Expand All @@ -38,30 +38,23 @@ EOF

# install shiny and other R packages used by the OHDSI PatientLevelPrediction R package viewPLP() function
# and additional model related R packages
RUN install2.r \
DT \
markdown \
plotly \
shiny \
shinycssloaders \
shinydashboard \
shinyWidgets \
xgboost \
RUN install2.r --error --skipinstalled --repos "https://packagemanager.posit.co/cran/latest" \
DT \
markdown \
plotly \
shiny \
shinycssloaders \
shinydashboard \
shinyWidgets \
xgboost \
&& rm -rf /tmp/download_packages/ /tmp/*.rds

# install the jdbc drivers for database access using the OHDSI DatabaseConnector R package
ENV DATABASECONNECTOR_JAR_FOLDER="/opt/hades/jdbc_drivers"
RUN R <<EOF
library(DatabaseConnector);
downloadJdbcDrivers('postgresql');
downloadJdbcDrivers('redshift');
downloadJdbcDrivers('sql server');
downloadJdbcDrivers('oracle');
downloadJdbcDrivers('spark');
EOF
RUN R -e "DatabaseConnector::downloadJdbcDrivers('all');"

# Install Rserve server and client
RUN install2.r \
RUN install2.r --error --skipinstalled --repos "https://packagemanager.posit.co/cran/latest" \
Rserve \
RSclient \
&& rm -rf /tmp/download_packages/ /tmp/*.rds
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