Merge pull request #45 from daisybio/new_dockerfile

changed Dockerfile to using conda with custom base image

Dockerfile

@@ -1,32 +1,19 @@
-FROM python:3.12.6-bullseye
-
-# Install required packages using apt
-# RUN apt-get update && apt-get install -y \
-#     libmariadb3 libmariadb-dev build-essential linux-headers-amd64 mariadb-connector-c \
-#     && rm -rf /var/lib/apt/lists/*
+FROM community.wave.seqera.io/library/bioconductor-gsva_bioconductor-sponge_gunicorn_python_pruned:e9c5176f69f5398d
 
+# Install required system dependencies for MySQL, R, and Conda
 RUN apt-get update && apt-get install -y \
-    default-mysql-client default-libmysqlclient-dev build-essential linux-headers-amd64 \
+    default-mysql-client pkg-config default-libmysqlclient-dev build-essential \
     && rm -rf /var/lib/apt/lists/*
 
-# Upgrade pip
-RUN pip3 install --upgrade pip
 
+# Install Python dependencies
 WORKDIR /server
-COPY . /server
-
-RUN pip3 --no-cache-dir install -r requirements.txt
-RUN pip install debugpy
+COPY requirements.txt /server/requirements.txt
+RUN micromamba run pip install --no-cache-dir -r requirements.txt
 
+# Copy application code
+COPY . /server
 
-# the mariadb plugin directory seems to be misconfigured
-# bei default. In order to work properly we manually adjust
-# the path.
-# ENV MARIADB_PLUGIN_DIR /usr/lib/mariadb/plugin
-
-# EXPOSE 5000
-# CMD ["python3", "server.py"]
-
-#run the command to start uWSGI
+# Start the application using gunicorn with UvicornWorker
 CMD ["gunicorn", "-k", "uvicorn.workers.UvicornWorker", "-b", "0.0.0.0:5000", "-w", "4", "server:connex_app"]