Skip to content
Snippets Groups Projects
Commit 6a3ee355 authored by Studer Gabriel's avatar Studer Gabriel
Browse files

updated Dockerfile

parent b20db1d8
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 34 additions and 88 deletions
docker/Dockerfile
+ 34
− 88
View file @ 6a3ee355
......@@ -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"]
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment