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LigParGen Docker Container
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# 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" |
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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.