From e9dbd950e84117083c3294f398002130969085ed Mon Sep 17 00:00:00 2001
From: Fortune Iriaye <firiaye@uab.edu>
Date: Mon, 24 Feb 2025 10:28:02 -0600
Subject: [PATCH] Update Dockerfile to implement multi-stage build
---
docker/Dockerfile | 33 +++++++++++++++++++--------------
1 file changed, 19 insertions(+), 14 deletions(-)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index f2f6849..694fd1a 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM tensorflow/tensorflow:1.15.0 AS tensorflow
# Set noninteractive mode to prevent prompts during installation
ENV DEBIAN_FRONTEND=noninteractive
@@ -10,7 +10,7 @@ RUN apt-get update && apt-get install -y \
curl \
git \
build-essential \
- libcurl4-openssl-dev \
+ libcurl4-openssl-dev || apt-get install -y libcurl4-gnutls-dev \
libssl-dev \
libxml2-dev \
libxt-dev \
@@ -22,13 +22,6 @@ RUN apt-get update && apt-get install -y \
psmisc \
&& rm -rf /var/lib/apt/lists/*
-# Create an RStudio user with sudo access
-RUN useradd -m -s /bin/bash rstudio && echo "rstudio:rstudio" | chpasswd && \
- usermod -aG sudo rstudio
-
-# Set working directory
-WORKDIR /root
-
# Install Miniconda
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
bash miniconda.sh -b -p /opt/miniconda && \
@@ -42,7 +35,6 @@ RUN echo "channels:\n - conda-forge\n - bioconda\n - defaults\n - r" > /root
# Create Conda environment and install dependencies
RUN conda create --name neuroestimator -y \
- r-essentials \
tensorflow=1.15.0 \
tensorflow-estimator=1.15.1 \
r-keras=2.3.0.0 \
@@ -54,10 +46,23 @@ RUN conda create --name neuroestimator -y \
r-remotes \
'r-reticulate<=1.24'
-# Install RStudio Server
-RUN wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.12.1-563-amd64.deb -O rstudio-server.deb && \
- dpkg -i rstudio-server.deb || apt-get -f install -y && \
- rm rstudio-server.deb
+# Rstudio setup
+FROM rocker/rstudio:4.3.3 AS rstudio
+
+# Set environment variables
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PATH="/opt/miniconda/bin:$PATH"
+
+# Copy Tensorflow and Miniconda environment
+COPY --from=tensorflow /opt/miniconda /opt/miniconda
+COPY --from=tensorflow /root/.condarc /root/.condarc
+
+# Create an Rstudio User
+
+RUN id -u rstudio >/dev/null 2>&1 || useradd -m -s /bin/bash rstudio && \
+ echo "rstudio:rstudio" | chpasswd && \
+ usermod -aG sudo rstudio
# Ensure RStudio uses Conda's R
RUN echo 'export RSTUDIO_WHICH_R="/opt/miniconda/envs/neuroestimator/bin/R"' >> /etc/profile.d/rstudio.sh
--
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