# Use the specific base image
FROM ubuntu:jammy-20221130

# GHCR related label
LABEL org.opencontainers.image.source=https://github.com/id-bioinfo/TIPars
LABEL org.opencontainers.image.description="TIPars - Taxa Insertion by Parsimony on Ubuntu Jammy"
LABEL org.opencontainers.image.licenses=LGPL-2.1

# Set up a new user named "user" with user ID 1000
RUN useradd -m -u 1000 user

# Set up environment variables for the user
ENV HOME=/home/user \
    PATH=/home/user/.local/bin:$PATH

# Set the working directory to the user's home directory
WORKDIR $HOME/app

# Install Java
RUN apt-get update && apt-get install -y openjdk-11-jdk

# Set the JAVA_HOME environment variable
ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64

# Update apt and apt-get
RUN apt-get update
RUN apt update
RUN apt upgrade -y

# Install java JRE
RUN apt install default-jre -y

# Setting timezone for installing python without manual user input
ENV TZ=Asia/Hong_Kong
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
# Install deadsnakes for python installation
RUN apt install software-properties-common -y
RUN add-apt-repository ppa:deadsnakes/ppa -y
# Install python3.11
RUN apt install python3.11 -y
# Install pip3
RUN apt install python3-pip -y
# Update python3 command to use python3.11 instead of 3.10
RUN update-alternatives --install /usr/bin/python3 python /usr/bin/python3.11 10

# Install Perl and Perl libraries 
RUN apt install perl -y
RUN apt-get install libtime-hires-perl -y
RUN apt install libdata-dump-perl -y

# Install ete3 w/ pip
RUN python3.11 -m pip install six numpy
RUN python3.11 -m pip install ete3

# Install pastml w/ pip
RUN python3.11 -m pip install pastml

# Install gcc and OpenMP
RUN apt install gcc -y
RUN apt-get install libomp-dev -y

# Change ownership of the working directory to the user
RUN chown -R user:user $HOME/app

# Switch to the user
USER user

# Copy all files to the working directory
# COPY ./ $HOME/app/
# Copy all files to the working directory with correct ownership
COPY --chown=user:user ./ $HOME/app/

# Install required Python dependencies
RUN python3.11 -m pip install -r $HOME/app/requirements.txt

# Install mafft
# RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz
# RUN tar xfvz mafft-7.520-linux.tgz

# Expose the desired port
EXPOSE 7860

# Set the command to run the Python application
CMD ["python3.11", "app.py"]

# CMD ["tipars/tipars", "-t", "tipars/Benchmark_datasets/NDV/NDV_tree.nwk", "-s", "tipars/Benchmark_datasets/NDV/NDV_taxa.fas", "-a", "tipars/Benchmark_datasets/NDV/NDV_anc.fas", "-q", "tipars/Benchmark_datasets/NDV/NDV_query.fas", "-o", "tipars/Benchmark_datasets/NDV/tipars.tree"]