Dockerfile

Dockerfile

@@ -0,0 +1,73 @@
+# Use the official Ubuntu image as a parent image
+FROM ubuntu:latest
+
+# Avoid interactive dialog during package installations
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Install necessary packages
+RUN apt-get update -y && \
+    apt-get install -y vim wget git
+
+# Set environment variables
+ENV CONDA_HOME=/opt/conda
+ENV PATH=$CONDA_HOME/bin:$PATH
+
+# Install Miniconda
+RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh && \
+    bash miniconda.sh -b -p $CONDA_HOME && \
+    rm miniconda.sh
+
+# Set the working directory
+WORKDIR /opt
+
+# Create a Conda environment and install dependencies
+RUN /opt/conda/bin/conda create -n myenv -y python=3.8
+RUN /opt/conda/bin/conda init bash
+RUN echo "conda activate myenv" >> ~/.bashrc
+ENV PATH=$CONDA_HOME/envs/myenv/bin:$PATH
+
+# Install additional Python packages directly
+RUN conda install -n myenv -y -c anaconda scipy=1.7 pandas=1.5 'numpy<1.23.0'
+RUN /opt/conda/envs/myenv/bin/pip install rdkit
+RUN conda install -n myenv -y -c conda-forge openbabel
+RUN conda install -n myenv -y anaconda::networkx anaconda::tqdm anaconda::tabulate
+
+## Install packmol
+# Clone Packmol repository
+RUN apt-get install -y build-essential gfortran
+RUN git clone https://github.com/m3g/packmol.git /opt/packmol
+WORKDIR /opt/packmol
+RUN make
+
+# Set the PACKMOL_EXEC environment variable
+ENV PACKMOL_EXEC=/opt/packmol/packmol
+
+## Install pysimm
+WORKDIR /opt
+RUN git clone -b 1.1 --single-branch https://github.com/polysimtools/pysimm 
+# Set up PYTHONPATH
+ENV PYTHONPATH=$PYTHONPATH:/opt/pysimm
+# Set up PATH
+ENV PATH=$PATH:/opt/pysimm/bin
+
+## Install ambertools
+RUN conda install -n myenv -y -c conda-forge ambertools
+ENV ANTECHAMBER_EXEC=/opt/conda/envs/myenv/bin/antechamber
+
+## Install PSP
+RUN git clone https://github.com/Ramprasad-Group/PSP.git
+WORKDIR /opt/PSP
+RUN /opt/conda/envs/myenv/bin/python setup.py install
+
+# Set up default Python to /opt/conda/envs/myenv/bin/python
+RUN echo 'export PATH=/opt/conda/envs/myenv/bin:$PATH' >> /etc/profile.d/python.sh && \
+    echo 'alias python=/opt/conda/envs/myenv/bin/python' >> /etc/profile.d/python.sh
+
+# Set HOME as working directory
+WORKDIR /root
+
+# Copy test files to /root
+RUN cp -r /opt/PSP/test/ /root/
+
+# Set the default command to run your application
+CMD ["bash"]