add dockerfile rstudio

Author: jwijffels

.github/workflows/build.yml

@@ -18,7 +18,8 @@ jobs:
           - { tag: "base-apps", dockerfile: "apps/Dockerfile", context: "apps"}
           - { tag: "inception-minio", dockerfile: "inception/inception-minio/Dockerfile", context: "inception/inception-minio"}
           - { tag: "inception-minio-mariadb", dockerfile: "inception/inception-minio-mariadb/Dockerfile", context: "inception/inception-minio-mariadb"}
-          - { tag: "shinyproxy", dockerfile: "shinyproxy/Dockerfile", context: "shinyproxy"}          
+          - { tag: "shinyproxy", dockerfile: "shinyproxy/Dockerfile", context: "shinyproxy"}    
+          - { tag: "rstudio", dockerfile: "development/rstudio/Dockerfile", context: "development/rstudio"}                
           - { tag: "prefect-example", dockerfile: "test/prefectexample/Dockerfile", context: "test/prefectexample"}
           - { tag: "prefect-inspect", dockerfile: "test/prefectinspect/Dockerfile", context: "test/prefectinspect"}
 

development/rstudio/03_setup_root_path.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/with-contenv bash
+
+echo "root path: $WWW_ROOT_PATH"
+
+if [[ ! -z $WWW_ROOT_PATH ]]
+then
+        echo "Set www-root-path to $WWW_ROOT_PATH"
+        echo "www-root-path=$WWW_ROOT_PATH" >> /etc/rstudio/rserver.conf
+else
+        echo "Not setting www-root-path"
+fi
+
+

development/rstudio/04_copy_env.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/with-contenv bash
+
+printenv >> /home/$USER/.Renviron

development/rstudio/Dockerfile

@@ -0,0 +1,57 @@
+## Ubuntu 20.04 with RStudio
+FROM ghcr.io/rocker-org/rstudio:4.2.1 
+
+##
+## System requirements
+##
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+    wget \
+    libcurl4-openssl-dev \
+    libssl-dev \ 
+    curl \
+    bash \
+    git \
+    && rm -rf /var/lib/apt/lists/*
+
+##
+## Install Java 21 from eclipse-temurin (For connection to IRIS)
+##
+ENV JAVA_HOME=/opt/java/openjdk
+COPY --from=eclipse-temurin:21 ${JAVA_HOME} ${JAVA_HOME}
+ENV PATH="${JAVA_HOME}/bin:${PATH}"
+
+##
+## Intersystems database
+##
+RUN wget https://github.com/intersystems-community/iris-driver-distribution/raw/main/JDBC/JDK18/intersystems-jdbc-3.8.0.jar --output-document=intersystems-jdbc.jar
+
+##
+## Install uv
+## Install Python 3.10 and Python package dependencies
+##
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+    software-properties-common \
+    && rm -rf /var/lib/apt/lists/*
+RUN add-apt-repository ppa:deadsnakes/ppa
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+    python3.10 python3.10-dev python3.10-tk python3.10-distutils \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 1 && update-alternatives --config python3
+COPY requirements.txt .
+#RUN python3.10 -m pip install --no-cache-dir -r requirements.txt
+#RUN python3 -m pip install --no-cache-dir -r requirements.txt
+RUN uv pip install --system --no-cache-dir -r requirements.txt
+
+##
+## Rstudio initializations
+##
+# NB: this file is only used by rocker if the env var DISABLE_AUTH: true is specified in the application.yml
+RUN echo "www-frame-origin=same"   >> /etc/rstudio/disable_auth_rserver.conf
+RUN echo "www-verify-user-agent=0" >> /etc/rstudio/disable_auth_rserver.conf
+ADD 03_setup_root_path.sh /etc/cont-init.d/03_setup_root_path.sh
+ADD 04_copy_env.sh        /etc/cont-init.d/04_copy_env.sh

development/rstudio/requirements.txt

@@ -0,0 +1,23 @@
+## Backend
+pandas
+numpy<=1.26.4
+pycaprio @ git+https://github.com/JavierLuna/[email protected]#egg=pycaprio
+dkpro-cassis==0.9.1
+spacy
+torch
+biopython==1.83.0
+jaydebeapi
+minio
+podman
+attrs
+pydantic==1.10.11
+urllib3==1.26.15
+requests-toolbelt==0.10.1
+#prefect-ray
+prefect-dask
+faker==24.0.0
+dateparser==1.2.0
+babel==2.14.0
+python-dotenv==1.0.1
+## Frontend
+shiny>=0.9.0