LigParGen Docker Container

Dockerfile

# syntax=docker/dockerfile:1
FROM ubuntu 
RUN apt-get update 
RUN apt-get install tcsh 
RUN mkdir app
COPY boss0520.tar.gz app/boss0520.tar.gz 
WORKDIR "/app"
RUN tar xovf boss0520.tar.gz
RUN echo setenv BOSSdir /app/boss > ~/.cshrc 
RUN apt-get install wget -y
RUN  apt-get upgrade -y
RUN  dpkg --add-architecture i386
RUN  apt-get update -y
RUN  apt-get upgrade -y
RUN  apt-get install libc6-i386 -y
RUN  apt-get install libstdc++6:i386 -y
RUN  apt-get install libfontconfig1 libxrender1 -y 
RUN apt-get install unzip
ENV PATH="/root/miniconda3/bin:${PATH}"
ARG PATH="/root/miniconda3/bin:${PATH}"
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && mkdir /root/.conda \
    && bash Miniconda3-latest-Linux-x86_64.sh -b \
    && rm -f Miniconda3-latest-Linux-x86_64.sh \
    && echo "Running $(conda --version)" && \
    conda init bash && \
    . /root/.bashrc && \
    conda update conda && \
    conda create -n python-app && \
    conda activate python-app && \
    conda install python=3.6 pip && \
    echo 'print("Hello World!")' > python-app.py

SHELL ["conda", "run", "-n", "python-app", "/bin/bash", "-c"]
RUN python --version 
RUN pip install rdkit-pypi
RUN pip install networkx==1.11
RUN pip install cython
RUN apt-get update 
RUN apt-get install git --fix-missing -y 
RUN apt --fix-broken install -y 
RUN git clone https://github.com/leelasd/LigParGen_2.3.git
WORKDIR LigParGen_2.3
RUN pip install -e . 
RUN conda install openbabel -c openbabel 
ENV PATH=/root/miniconda3/envs/python-app/bin/:${PATH}
RUN apt-get update
RUN apt-get install libxtst6:i386 -y
RUN apt-get install libxtst6 -y
ENV BOSSdir="/app/boss"
RUN LigParGen -s 'c1ccc(cc1)O' -r PHN -c 0 -o 0  
WORKDIR "/home"

Installation Instructions for building the container on Mac OS. Make sure that Dockerfile is in the same directory when you are executing the command. Keep in mind that platform option needs to be changed based on how your system reacts, so be ready to play around with that.

docker build . -t lpg_docker_latest --platform linux/x86_64