Merge pull request #81 from Integrative-Transcriptomics/dev

Change to Ubuntu

Author: mwittep

celery/dockerfile

@@ -1,61 +1,57 @@
+FROM ubuntu:22.04
 
-# first stage build the frontend
-# FROM node:20-alpine3.18 as build
-FROM --platform=linux/x86_64 alpine:3.21.2
+# Set non-interactive mode for apt-get
+ENV DEBIAN_FRONTEND=noninteractive
 
-# Set the working directory in the container to /app
-# Set the working directory in the container to /app
-# WORKDIR /import
-# COPY .. .
-# Copy the current directory contents into the container at /app
-
-# COPY ../server_tsspredator .
-# COPY ../requirements.txt .
-# COPY ../setup.py .
-# COPY ../TSSpredator.jar .
-
-# RUN corepack enable
-# # Install Node.js dependencies
-# RUN npm run build
-
-
-# Set the working directory in the container to /app
+# Set the working directory
 WORKDIR /app
 
-# copy the server directory and dist from previous buildstage into the container at /app
+# Update package lists and install required packages
+RUN apt-get update && apt-get install -y \
+    wget \
+    gcc \
+    g++ \
+    python3-dev \
+    python3-venv \
+    python3-pip \
+    openjdk-17-jre-headless \
+    libbz2-dev \
+    libcurl4 \
+    libkrb5-dev \
+    zlib1g-dev \
+    curl \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy application files
 COPY server_tsspredator /app/server_tsspredator
 COPY requirements.txt /app
 COPY setup.py /app
 COPY server_tsspredator/TSSpredator.jar /app
-RUN apk add gcompat libbz2 libcurl libstdc++ krb5-dev zlib gcc musl-dev g++ curl-dev
-RUN wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig -P /app
-RUN chmod +x /app/bedGraphToBigWig
-
-# Install java 17
-RUN apk add --update --no-cache openjdk17-jre-headless
 
+# Download bedGraphToBigWig and set execute permissions
+RUN wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig -P /app && \
+    chmod +x /app/bedGraphToBigWig
 
-# Install python3.11
-RUN apk add --update --no-cache python3-dev py3-pip
+# Create a Python virtual environment and install dependencies
 RUN python3 -m venv /app/env_tss_predator_celery
 ENV PATH="/app/env_tss_predator_celery/bin:$PATH"
-RUN python3 -m pip install --upgrade pip
-# install python dependencies
-RUN python3 -m pip install -r requirements.txt
+RUN python3 -m pip install --upgrade pip && \
+    python3 -m pip install -r requirements.txt
 
-# Install the server package
+# Install the server package in editable mode
 RUN pip install -e .
 
-# Make port 5001 available to the world outside this container
+# Clean up build files
+RUN rm -rf /app/requirements.txt /app/setup.py
+
+# Expose the application port
 EXPOSE 5001
+
+# Set environment variables
 ENV TSSPREDATOR_DATA_PATH="/data"
 ENV TSSPREDATOR_SERVER_LOCATION="/app"
 ENV TSSPREDATOR_TEMPDATA="/tmpData"
 ENV TSSPREDATOR_REDIS_HOST="redis"
 
-RUN rm -rf /app/requirements.txt 
-RUN rm -rf /app/setup.py
-
-
-# The command that will be executed when the container is run
-CMD ["gunicorn","--workers", "6","--timeout","500","--graceful-timeout", "500", "--bind", "0.0.0.0:5001", "wsgi:tsspredator"]
+# Run the application via gunicorn
+CMD ["gunicorn", "--workers", "6", "--timeout", "500", "--graceful-timeout", "500", "--bind", "0.0.0.0:5001", "wsgi:tsspredator"]