diff --git a/docker/Dockerfile b/docker/Dockerfile
index a02301453bc4c02b5cbb0de4a2948d64f2d15d0e..3846bddbdb2133d5011d1c3782068d66f3ffbbce 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -2,67 +2,47 @@ FROM ubuntu:18.04
# ARGUMENTS
###########
-
-ARG OPENSTRUCTURE_VERSION="1.10.0"
+ARG OPENSTRUCTURE_VERSION="python3_port"
ARG SRC_FOLDER="/usr/local/src"
-ARG CPUS_FOR_MAKE=8
-ARG PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
+ARG CPUS_FOR_MAKE=2
ARG OPENSTRUCTURE_SHARE="/usr/local/share/ost"
ARG MSMS_VERSION="2.6.1"
ARG OPENMM_VERSION="7.1.1"
-ARG DSSP_VERSION="2.2.1"
ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/"
ARG OPENMM_LIB_PATH="/usr/local/openmm/lib/"
+ARG DEBIAN_FRONTEND=noninteractive
# INSTALL SYSTEM DEPS
#####################
RUN apt-get update -y && apt-get install -y cmake \
g++ \
+ gfortran \
+ wget \
+ tar \
+ libsqlite3-dev \
sip-dev \
libtiff-dev \
libfftw3-dev \
libeigen3-dev \
libboost-all-dev \
libpng-dev \
- python-all \
- python2.7 \
- python-pyqt5 \
qt5-qmake \
qtbase5-dev \
- wget \
- git \
- gfortran \
- python-pip \
- tar \
- libbz2-dev \
+ python3-all \
+ python3-pyqt5 \
+ python3-numpy \
+ python3-scipy \
+ python3-pandas \
doxygen \
swig \
clustalw \
- python-virtualenv \
- libsqlite3-dev \
dssp \
- python-enum34 \
locales && \
# CLEANUP
rm -rf /var/lib/apt/lists/*
-# INSTALL SOME PYTHON PACKAGES GLOBALY
-######################################
-RUN pip install -U pip==9.0.3 && \
- pip install -U setuptools==39.0.1 && \
- pip install --no-cache-dir numpy==1.10.4 \
- scipy==1.0.0 \
- pandas==0.22.0
-
-# SET LOCALE
-############
-# RUN echo "LC_ALL=en_US.UTF-8" >> /etc/environment
-# RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
-# RUN echo "LANG=en_US.UTF-8" > /etc/locale.conf
-# RUN locale-gen en_US.UTF-8
-
-# DOWNLOAD AND INSTALL MSMS
-###########################
+# INSTALL MSMS
+##############
RUN cd ${SRC_FOLDER} && \
mkdir -p msms && \
cd ${SRC_FOLDER}/msms && \
@@ -73,8 +53,8 @@ RUN cd ${SRC_FOLDER} && \
cp -v ${SRC_FOLDER}/msms/pdb_to_xyzrn /usr/local/bin/pdb_to_xyzrn && \
rm -rf ${SRC_FOLDER}/msms
-# COMPILE OPENMM FROM SOURCES. INSTALL TO /usr/local
-####################################################
+# INSTALL OPENMM
+################
RUN cd ${SRC_FOLDER} && \
wget -O openmm-${OPENMM_VERSION}.tar.gz -nc https://github.com/pandegroup/openmm/archive/${OPENMM_VERSION}.tar.gz && \
mkdir ${SRC_FOLDER}/openmm-${OPENMM_VERSION} && \
@@ -83,23 +63,20 @@ RUN cd ${SRC_FOLDER} && \
cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && \
cmake .. && make -j $CPUS_FOR_MAKE && make install && \
cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build/python && \
- python setup.py build && python setup.py install && \
- rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
+ python3 setup.py build && python3 setup.py install && \
+ rm ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
# INSTALL OST
#############
RUN cd ${SRC_FOLDER} && \
-# copy ost release
+ # copy ost release
wget -O openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/openstructure/repository/${OPENSTRUCTURE_VERSION}/archive.tar.gz && \
mkdir openstructure-${OPENSTRUCTURE_VERSION} && \
tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1 && \
- mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
-
-WORKDIR ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
-
-# cmake ost
-RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
+ mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
+ cd ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
+ cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
-DOPTIMIZE=ON \
-DENABLE_MM=ON \
-DCOMPILE_TMTOOLS=1 \
@@ -109,52 +86,21 @@ RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
-DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
-DENABLE_GFX=ON \
-DENABLE_GUI=ON && \
- # Build chemdict_tool
- make -j ${CPUS_FOR_MAKE} chemdict_tool
-
-# get the compound library
-RUN wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz
-RUN stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm
-RUN mkdir -p $OPENSTRUCTURE_SHARE && chmod a+rw -R $OPENSTRUCTURE_SHARE && mv compounds.chemlib $OPENSTRUCTURE_SHARE
-
-# Build and install OST
-RUN cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
- -DOPTIMIZE=ON \
- -DENABLE_MM=ON \
- -DCOMPILE_TMTOOLS=1 \
- -DUSE_NUMPY=1 \
- -DOPEN_MM_LIBRARY=$OPENMM_LIB_PATH/libOpenMM.so \
- -DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
- -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
- -DENABLE_GFX=ON \
- -DENABLE_GUI=ON \
- -DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/compounds.chemlib && \
- # Build OST with compound library
- make -j ${CPUS_FOR_MAKE} && make check && make install
-
-# GO HOME AND CLEANUP
-#####################
-# RUN apt-get purge -y cmake \
-# wget \
-# git \
-# gfortran \
-# python-pip \
-# libbz2-dev \
-# doxygen \
-# swig
-# RUN apt-get clean
-# RUN apt-get autoremove -y
-#
-# WORKDIR $SRC_FOLDER
-# RUN rm -rf $SRC_FOLDER/*
-
-WORKDIR /home
+ make -j ${CPUS_FOR_MAKE} && \
+ wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz && \
+ stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm && \
+ mkdir -p $OPENSTRUCTURE_SHARE && chmod a+rw -R $OPENSTRUCTURE_SHARE && mv compounds.chemlib $OPENSTRUCTURE_SHARE && \
+ cmake .. -DCOMPOUND_LIB=$OPENSTRUCTURE_SHARE/compounds.chemlib && \
+ make -j ${CPUS_FOR_MAKE} && make check && make install && \
+ rm ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}.tar.gz && \
+ rm -rf ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}
# ENVIRONMENT
-##############################################################################
+#############
+WORKDIR /home
ENV OST_ROOT="/usr/local"
-ENV PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
-ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64"
+ENV PYTHONPATH="/usr/local/lib64/python3.6/site-packages"
+ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:/usr/local/openmm/lib/"
ENV QT_X11_NO_MITSHM=1
ENTRYPOINT ["ost"]