Dockerfile

# Using the a base image of rmgpy:latest from DockerHub - Not the official version but a custom version that is smaller in size
FROM --platform=linux/amd64 laxzal/arc:latest

USER rmguser

# Installing ARC
# Change directory to Code
WORKDIR /home/rmguser/Code

# Install T3

# Change directory to Code
WORKDIR /home/rmguser/Code

# Clone main branch T3 repository from GitHub and set as working directory
RUN git clone -b main https://github.com/ReactionMechanismGenerator/T3.git
WORKDIR /home/rmguser/Code/T3

# Install T3 Environment
RUN micromamba create -y -f environment.yml && \
    micromamba clean --all -f -y && \
    rm -rf /home/rmguser/.cache/yarn \
    rm -rf /home/rmguser/.cache/pip \
    && find -name '__pycache__' -type d -exec rm -rf '{}' '+' && \
    find /opt/conda/envs/t3_env/lib/python3.7/site-packages/scipy -name 'tests' -type d -exec rm -rf '{}' '+' && \
    find /opt/conda/envs/t3_env/lib/python3.7/site-packages/numpy -name 'tests' -type d -exec rm -rf '{}' '+' && \
    find /opt/conda/envs/t3_env/lib/python3.7/site-packages/pandas -name 'tests' -type d -exec rm -rf '{}' '+' && \
    find /opt/conda/envs/t3_env/lib/python3.7/site-packages -name '*.pyx' -delete \
    && find /opt/conda/ -follow -type f -name '*.a' -delete \
    && find /opt/conda/ -follow -type f -name '*.pyc' -delete \
    && find /opt/conda/ -follow -type f -name '*.js.map' -delete

# Add alias to bashrc - rmge to activate the environment
# These commands are not necessary for the Docker image to run, but they are useful for the user
RUN echo "export arc_path='/home/rmguser/Code/ARC/'" >> ~/.bashrc \
    && echo "export t3_path='/home/rmguser/Code/T3/'" >> ~/.bashrc \
    && echo "alias t3code='cd \$t3_path'" >> ~/.bashrc \
    && echo "alias t3e='micromamba activate t3_env'" >> ~/.bashrc \
    && echo "alias t3='python /home/rmguser/Code/T3/T3.py input.yml'" >> ~/.bashrc

# Set the wrapper script as the entrypoint
ENTRYPOINT ["/home/rmguser/entrywrapper.sh"]

# Activate the T3 environment
WORKDIR /home/rmguser/
ARG MAMBA_DOCKERFILE_ACTIVATE=1
ENV ENV_NAME=t3_env