Updated borad sanger docker images

Author: jjacobson95

build/docker/Dockerfile.broad_sanger_exp

@@ -1,31 +1,32 @@
 FROM r-base:4.4.1
-ENV DEBIAN_FRONTEND=noninteractive
-RUN apt-get update  --fix-missing
-#RUN apt-get install -y --fix-missing --allow-unauthenticated build-essential libpq-dev python3.10 python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libxml2-dev libglpk-dev
-
-# RUN apt-get install -y --fix-missing --allow-unauthenticated build-essential python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libglpk-dev libxml2-dev libpq-dev
-
-RUN apt-get install -y --fix-missing --allow-unauthenticated \
-    build-essential \
-    python3-pip \
-    python3-setuptools \
-    python3-dev \
-    python3-venv \
-    libcurl4-openssl-dev \
-    libglpk-dev \
-    libxml2-dev \
-    libpq-dev \
-    ca-certificates
-
-RUN python3 -m venv /opt/venv
-RUN /opt/venv/bin/pip3 install --upgrade pip
 
+ENV DEBIAN_FRONTEND=noninteractive
 
-# Set MPLCONFIGDIR to a writable directory
+# Update and upgrade packages, then install required packages.
+RUN apt-get update --fix-missing && \
+    apt-get upgrade -y && \
+    apt-get install -y --fix-missing --allow-unauthenticated \
+      build-essential \
+      python3-pip \
+      python3-setuptools \
+      python3-dev \
+      python3-venv \
+      libcurl4-openssl-dev \
+      libglpk-dev \
+      libxml2-dev \
+      libpq-dev \
+      ca-certificates && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Create and upgrade the Python virtual environment.
+RUN python3 -m venv /opt/venv && \
+    /opt/venv/bin/pip install --upgrade pip
+
+# Set MPLCONFIGDIR to a writable directory and create it.
 ENV MPLCONFIGDIR=/app/tmp/matplotlib
 RUN mkdir -p /app/tmp/matplotlib
 
-
+# Set Python path and working directory.
 ENV PYTHONPATH "${PYTHONPATH}:/app"
 WORKDIR /app
 

build/docker/Dockerfile.broad_sanger_omics

@@ -1,32 +1,36 @@
 FROM r-base:4.4.1
+
 ENV DEBIAN_FRONTEND=noninteractive
-RUN apt-get update  --fix-missing
-
-# RUN apt-get install -y --fix-missing --allow-unauthenticated build-essential python3-pip python3-setuptools python3-dev python3-venv libcurl4-openssl-dev libglpk-dev libxml2-dev libpq-dev
-
-RUN apt-get install -y --fix-missing --allow-unauthenticated \
-    build-essential \
-    python3-pip \
-    python3-setuptools \
-    python3-dev \
-    python3-venv \
-    libcurl4-openssl-dev \
-    libglpk-dev \
-    libxml2-dev \
-    libpq-dev \
-    ca-certificates
-
-RUN python3 -m venv /opt/venv
-RUN /opt/venv/bin/pip3 install --upgrade pip
-
-# Set MPLCONFIGDIR to a writable directory
+
+# Update and upgrade packages, then install required packages.
+RUN apt-get update --fix-missing && \
+    apt-get upgrade -y && \
+    apt-get install -y --fix-missing --allow-unauthenticated \
+      build-essential \
+      python3-pip \
+      python3-setuptools \
+      python3-dev \
+      python3-venv \
+      libcurl4-openssl-dev \
+      libglpk-dev \
+      libxml2-dev \
+      libpq-dev \
+      ca-certificates && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Create and upgrade the Python virtual environment.
+RUN python3 -m venv /opt/venv && \
+    /opt/venv/bin/pip install --upgrade pip
+
+# Set MPLCONFIGDIR to a writable directory and create it.
 ENV MPLCONFIGDIR=/app/tmp/matplotlib
 RUN mkdir -p /app/tmp/matplotlib
 
-
+# Set Python path and working directory.
 ENV PYTHONPATH "${PYTHONPATH}:/app"
 WORKDIR /app
 
+# Add application files.
 ADD build/broad_sanger/01-broadSangerSamples.R ./
 ADD build/broad_sanger/02-broadSangerOmics.R ./
 ADD build/broad_sanger/02a-broad_sanger_proteomics.py ./
@@ -40,14 +44,8 @@ ADD build/broad_sanger/05b_separate_datasets.py ./
 ADD build/broad_sanger/requirements.txt .
 ADD build/broad_sanger/omics_requirements.r .
 
-# installing r libraries
+# Install R libraries.
 RUN Rscript omics_requirements.r
 
-# installing python libraries
-RUN /opt/venv/bin/pip3 install -r requirements.txt
-
-
-
-
-
-
+# Install Python libraries.
+RUN /opt/venv/bin/pip install -r requirements.txt