Update Dockerfile

Author: gobikrishnan-s3141

Dockerfile

@@ -1,13 +1,40 @@
-FROM python:3
+# Python base image [pre-built ubuntu-base python env]
+FROM python:3.12-slim
 
-# Install required Python libraries
-RUN pip install numpy pandas matplotlib
+# reduce package overhead
+ENV DEBIAN_FRONTEND=noninteractive \
+    TZ=UTC \
+    PYTHONDONTWRITEBYTECODE=1 \
+    PYTHONUNBUFFERED=1 \
+    PIP_NO_CACHE_DIR=1 \
+    APP_HOME=/opt/MoVana
 
-# Set the working directory
-WORKDIR ~/MoVana
+# install dependencies
+RUN apt-get update &&  apt-get install -y --no-install-recommends build-essential \
+        wget \
+        git \
+        bedtools \
+        bcftools \
+        openjdk-17-jdk \
+        gfortran \
+        zlib1g-dev && \
+        rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# workspace
+RUN mkdir -p $APP_HOME
+
+# Setup Working directory`
+WORKDIR $APP_HOME
 
 # Copy the WDL script into the container
-COPY . ~/MoVana
+COPY . $APP_HOME
+
+# Cromwell (make sure Java is installed)
+RUN mkdir -p cromwell && wget https://github.com/broadinstitute/cromwell/releases/download/90/cromwell-90.jar && mv cromwell-90.jar cromwell/
+
+# python pkgs
+#RUN python3 -m venv 0env && source 0env/bin/activate && \
+RUN python3 -m pip install --upgrade pip setuptools wheel && python3 -m pip install --no-cache-dir pandas numpy matplotlib
 
-# Set the entry point
-ENTRYPOINT ["python3"]
+# Set login shell
+CMD ["/bin/bash -c"]