Update Dockerfile (#162)

* Update Dockerfile

Dockerfile

@@ -1,86 +1,23 @@
-FROM ubuntu:18.04 AS builder
-
-ARG OPENBABEL_TAG="openbabel-3-0-0"
-ARG RDKIT_TAG="Release_2019_09_3"
-ARG MMTF_TAG="v1.0.0"
-ARG PYMOL_TAG="v2.3.0"
+FROM debian:stable
 
 LABEL maintainer="PharmAI GmbH <contact@pharm.ai>" \
         org.label-schema.name="PLIP: The Protein-Ligand Interaction Profiler" \
         org.label-schema.description="https://www.doi.org/10.1093/nar/gkv315"
 
+ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update && apt-get install -y \
-    cmake \
-    git \
-    g++ \
-    imagemagick \
-    libboost-all-dev \
-    libeigen3-dev \
-    libfreetype6-dev \
-    libghc-zlib-dev \
-    libglew-dev \
-    libglm-dev \
-    libmsgpack-dev \
-    libnetcdf-dev \
-    libxml2-dev \
-    libpng-dev \
-    libpython3-all-dev \
-    python3 \
+    pymol \
+    python3-distutils \
     python3-lxml \
-    python3-numpy \
-    python3-pyqt5.qtopengl \
-    swig
-
-# build OpenBabel
-WORKDIR /src
-RUN git clone -b $OPENBABEL_TAG \
-    https://github.com/openbabel/openbabel.git
-WORKDIR /src/openbabel/build
-RUN cmake .. \
-    -DPYTHON_EXECUTABLE=/usr/bin/python3.6 \
-    -DPYTHON_BINDINGS=ON \
-    -DCMAKE_INSTALL_PREFIX=/usr/local \
-    -DRUN_SWIG=ON
-RUN make -j$(nproc --all) install
-
-# build RDkit
-#WORKDIR /src
-#RUN git clone -b $RDKIT_TAG \
-#    https://github.com/rdkit/rdkit.git
-#WORKDIR /src/rdkit/build
-#RUN cmake .. \
-#    -DCMAKE_BUILD_TYPE=Release \
-#    -DRDK_BUILD_INCHI_SUPPORT=ON \
-#    -DPYTHON_LIBRARY=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
-#    -DPYTHON_INCLUDE_DIR=/usr/include/python3.6 \
-#    -DPYTHON_EXECUTABLE=/usr/bin/python3.6
-#RUN make -j$(nproc --all) install
-#ENV RDBASE /src/rdkit
-#ENV LD_LIBRARY_PATH /usr/local/lib/:$RDBASE/lib
-#ENV PYTHONPATH $PYTHONPATH:$RDBASE
-
-# build mmtf-cpp
-WORKDIR /src
-RUN git clone -b $MMTF_TAG \
-    https://github.com/rcsb/mmtf-cpp.git
-WORKDIR /src/mmtf-cpp/build
-RUN cmake ..
-RUN make -j$(nproc --all) install
-
-# build PyMOL
-WORKDIR /src
-RUN git clone -b $PYMOL_TAG \
-    https://github.com/schrodinger/pymol-open-source
-WORKDIR /src/pymol-open-source
-RUN python3 setup.py build install \
-    --prefix=/usr/local \
-    --jobs=$(nproc --all)
+    python3-openbabel \
+    python3-pymol; \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # copy PLIP source code
 WORKDIR /src
 ADD plip/ plip/
 RUN chmod +x plip/plipcmd.py
-ENV PYTHONPATH $PYTHONPATH:/src
+ENV PYTHONPATH=/src
 
 # execute tests
 WORKDIR /src/plip/test
@@ -89,4 +26,4 @@ RUN ./run_all_tests.sh
 WORKDIR /
 
 # set entry point to plipcmd.py
-ENTRYPOINT  ["python3", "/src/plip/plipcmd.py"]
+ENTRYPOINT  ["python3", "/src/plip/plipcmd.py"]