dockerimage from dockerhub

Dockerfile

@@ -13,20 +13,7 @@
 # Base image #
 ##############
 # Adds rstudio server, tiyverse, devtools to rocker/cuda
-FROM dvats-rstudio-base:latest
-
-RUN echo "--> Prior installations" \ 
-    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys A4B469963BF863CC \
-    set -e; \
-    apt-get update --fix-missing \
-    && apt-get install -y \
-    python3-pip wget bzip2 curl \
-    git sudo libarchive-dev libtiff5-dev zsh\
-    #python3 -m pip install --upgrade pip \
-    python3-venv libxt-dev \
-    && apt-get clean  \
-    && rm -rf /var/lib/apt/lists/* 
-
+FROM misantamaria/dvats-rstudio:0
 
 SHELL [ "/bin/bash", "--login", "-c" ]
 
@@ -37,18 +24,15 @@ RUN echo "--> ARGS"
 ARG USER_NAME=user \
     USER_ID=1000 \
     GROUP_ID \
-    WANDB_API_KEY \ 
     WANDB_ENTITY \
     WANDB_PROJECT \
-    GH_TOKEN 
+
 
 RUN echo "--> ARGS -> ENV"
 ENV USER_NAME=$USER_NAME \
     USER_ID=$USER_ID \
     GROUP_ID=$GROUP_ID \
     WANDB_ENTITY=$WANDB_ENTITY \
-    WANDB_API_KEY=$WANDB_API_KEY \
-    GH_TOKEN=$ghtoken \
     WANDB_PROJECT=$WANDB_PROJECT
 
 RUN echo "--> Setup ENV variables"
@@ -59,41 +43,10 @@ ENV RETICULATE_PYTHON_ENV=/home/${USER_NAME}/env \
     ENV_VARS=WANDB_ENTITY,WANDB_PROJECT,USER_NAME,USER_ID,GROUP_ID,PASSWORD,ROOT,CUDA_VISIBLE_DEVICES\
     HOME="/home/${USER_NAME}"
 
-###########
-# Volumes #
-###########
-
-
-
-
-## Install R packages
-
-# COPY docker/DESCRIPTION /tmp/
-COPY --chown=${USER_ID}:${GROUP_ID} docker/DESCRIPTION /tmp/
-
-RUN echo "--> Install R packages" \ 
-    R -e "devtools::install_deps('/tmp/', dependencies = TRUE)"
-
-## Reticulate configuration
-ENV ENV_PREFIX $HOME/env
-
-RUN echo "---> Make sudo & setup sudoers"
-RUN echo "$(id)"
-
-ARG RETICULATE_MINICONDA_PATH=/usr/local/share/r-miniconda
-ARG RETICULATE_PYTHON_ENV=/usr/virtualenvs/venv_shiny_app
-ENV RETICULATE_PYTHON=${RETICULATE_PYTHON_ENV}/bin/python/
-
 RUN echo "---> RETICULATE PYTHONS"
 RUN echo "RETICULATE_PYTHON_ENV=${RETICULATE_PYTHON_ENV}" >> ${HOME}/.Renviron
 RUN echo "RETICULATE_PYTHON=${RETICULATE_PYTHON}" >> ${HOME}/.Renviron
 
-RUN echo "---> Export W&B"
-## Export W&B environment variable to Rstudio
-
-ARG WANDB_API_KEY
-RUN echo "WANDB_API_KEY=${WANDB_API_KEY}" >> ${HOME}/.Renviron
-
 
 ENV MINICONDA_VERSION=4.10.3 \ 
 #ENV MINICONDA_VERSION=23.9.0 \ 
@@ -151,10 +104,6 @@ RUN chmod u+x /usr/local/bin/postBuild \
 
 RUN conda list --prefix ${ENV_PREFIX}
 
-
-
-
-
 RUN echo "--> rewrrite miniconda path"
 # Rewrite the miniconda path environment in case it has been redefined in the compose file
 RUN echo "RETICULATE_MINICONDA_PATH=${RETICULATE_MINICONDA_PATH}" >> ${HOME}/.Renviron
@@ -175,26 +124,16 @@ COPY --chown=${USER_ID}:${GROUP_ID} ../r_shiny_app $HOME/app
 COPY --chown=${USER_ID}:${GROUP_ID} ${LOCAL_DATA_PATH} $HOME/data/
 COPY --chown=${USER_ID}:${GROUP_ID} ../dvats ${HOME}/dvats
 
-#RUN echo "--> Setup miniconda & Mamba"
-
-#RUN echo ". ${HOME}miniconda3/etc/profile.d/conda.sh" >> ${HOME}/rstudio/.bashrc
-
-
-#RUN echo "--> Conda activate"
-# Make bash automatically activate the conda environment
-#RUN echo "conda activate ${ENV_PREFIX}" >> ${HOME}/rstudio/.bashrc
-#echo "export WANDB_ENTITY=${WANDB_ENTITY:-default}" >> ${HOME}/.bashrc
-# echo "WANDB_ENTITY=${WANDB_ENTITY:-default}" >> ${HOME}/.Renviron
 
 # Define an array of environment variable names from the ENV_VARS Compose variable
-ARG ENV_VARS=ENV_VARS
-RUN echo "---> Setup variables" && \
-    IFS=',' read -ra NAMES <<< "ENV_VARS" && \
-    for ENV_VAR_NAsME in "${NAMES[@]}"; do \ 
+#ARG ENV_VARS=ENV_VARS
+#RUN echo "---> Setup variables" && \
+#    IFS=',' read -ra NAMES <<< "ENV_VARS" && \
+#    for ENV_VAR_NAsME in "${NAMES[@]}"; do \ 
     #echo "$ENV_VARS" | tr ',' '\n' | while read ENV_VAR_NAME; do \
-    ENV_VAR_VALUE="${!ENV_VAR_NAME:-default}"; \
-    echo "$ENV_VAR_NAME=$ENV_VAR_VALUE"; \
-    done > ${HOME}/.Renviron
+#    ENV_VAR_VALUE="${!ENV_VAR_NAME:-default}"; \
+#    echo "$ENV_VAR_NAME=$ENV_VAR_VALUE"; \
+#    done > ${HOME}/.Renviron
 
 # Install deepvats
 
@@ -203,4 +142,3 @@ RUN echo "--> Go!"
 
 CMD ["R", "--quiet", "-e", "shiny::runApp(host='0.0.0.0', port=${RSTUDIO_PORT:-3838}, launch.browser = FALSE, appDir = '/home/${USER_NAME}/app')"]
 
-# CMD ["/init"]