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Commit 1ddb7ab9 authored by Rafal Gumienny's avatar Rafal Gumienny
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fix: SCHWED-3096 Update for newest codebase

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docker/Dockerfile
+ 144
− 80
View file @ 1ddb7ab9
FROM ubuntu:16.04
# ARGUMENTS
###########
# OBLIGATORY
ARG OPENSTRUCTURE_VERSION
RUN if [ -z "${OPENSTRUCTURE_VERSION}" ]; then \
echo "OPENSTRUCTURE_VERSION argument is obligatory. Run with --build-arg OPENSTRUCTURE_VERSION=<VERSION>"; \
exit 1; \
else : ; fi
# OPTIONAL
ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=8
ARG PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
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/"
# INSTALL SYSTEM DEPS
#####################
RUN apt-get update -y && apt-get install -y cmake \
sip-dev \
libtiff-dev \
......@@ -17,97 +40,138 @@ RUN apt-get update -y && apt-get install -y cmake \
wget \
git \
gfortran \
libeigen3-dev \
python-pip \
tar \
libbz2-dev \
doxygen \
swig \
clustalw
# Install MSMS
WORKDIR /
RUN mkdir -p /msms
WORKDIR /msms
RUN wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL2.6.1/msms_i86_64Linux2_2.6.1.tar.gz
RUN tar -xvzf msms_i86_64Linux2_2.6.1.tar.gz
RUN ln -s /msms/msms.x86_64Linux2.2.6.1 /usr/bin/msms
RUN ln -s /msms/pdb_to_xyzr /usr/bin/pdb_to_xyzr
RUN ln -s /msms/pdb_to_xyzrn /usr/bin/pdb_to_xyzrn
# Install OpenMM
WORKDIR /
RUN git clone https://github.com/pandegroup/openmm
WORKDIR /openmm
RUN git checkout -b 7.1.1 tags/7.1.1
RUN cmake .
RUN make -j4
RUN make install
# Install DSSP
WORKDIR /
RUN wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.2.1.tgz
RUN tar -xvzf dssp-2.2.1.tgz
WORKDIR /dssp-2.2.1
RUN make
RUN ln -s /dssp-2.2.1/mkdssp /usr/bin/mkdssp
# Install some python packages
WORKDIR /
RUN pip install --upgrade pip && pip install numpy==1.10.4 \
scipy==1.0.0 \
pandas==0.22.0 \
jupyter==1.0.0
clustalw \
python-virtualenv \
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
###########################
RUN cd ${SRC_FOLDER} && \
mkdir -p msms && \
cd ${SRC_FOLDER}/msms && \
wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL${MSMS_VERSION}/msms_i86_64Linux2_${MSMS_VERSION}.tar.gz && \
tar -xvzf msms_i86_64Linux2_${MSMS_VERSION}.tar.gz && \
cp -v ${SRC_FOLDER}/msms/msms.x86_64Linux2.${MSMS_VERSION} /usr/local/bin/msms && \
cp -v ${SRC_FOLDER}/msms/pdb_to_xyzr /usr/local/bin/pdb_to_xyzr && \
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
####################################################
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} && \
tar xf openmm-${OPENMM_VERSION}.tar.gz -C ${SRC_FOLDER}/openmm-${OPENMM_VERSION} --strip-components=1 && \
mkdir -p ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && \
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 && \
rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
# COMPILE AND INSTALL DSSP
##########################
RUN cd ${SRC_FOLDER} && \
wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-${DSSP_VERSION}.tgz && \
tar -xvzf dssp-${DSSP_VERSION}.tgz && \
cd dssp-${DSSP_VERSION} && \
make -j ${CPUS_FOR_MAKE} && \
make install && \
rm -rf ${SRC_FOLDER}/dssp-${DSSP_VERSION}.tgz && \
rm -rf ${SRC_FOLDER}/dssp-${DSSP_VERSION}
# INSTALL OST
#############
RUN cd ${SRC_FOLDER} && \
# copy ost release
WORKDIR /opt/ost
RUN git clone https://git.scicore.unibas.ch/schwede/openstructure.git /opt/ost && git checkout -b develop origin/develop
# compile ost
RUN cmake . -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
-DOPTIMIZE=ON \
-DENABLE_MM=ON \
-DCOMPILE_TMTOOLS=1 \
-DUSE_NUMPY=1 \
-DOPEN_MM_LIBRARY=/usr/local/openmm/lib/libOpenMM.so \
-DOPEN_MM_INCLUDE_DIR=/usr/local/openmm/include \
-DOPEN_MM_PLUGIN_DIR=/usr/local/openmm/lib/plugins
# Build chemdict_tool
RUN make -j4 chemdict_tool
wget -O openstructure-${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 \
-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 && \
# 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
RUN stage/bin/chemdict_tool update modules/conop/data/charmm.cif compounds.chemlib charmm
# Reconfigure OST
RUN cmake . -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
-DOPTIMIZE=ON \
-DENABLE_MM=ON \
-DOPEN_MM_LIBRARY=/usr/local/openmm/lib/libOpenMM.so \
-DOPEN_MM_INCLUDE_DIR=/usr/local/openmm/include \
-DOPEN_MM_PLUGIN_DIR=/usr/local/openmm/lib/plugins \
-DCOMPOUND_LIB=/opt/ost/compounds.chemlib
# Build OST
RUN make -j4
RUN make check
# go back home
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 $SRC_FOLDER/*
WORKDIR /home
# Set the environment
# - for GUI
ENV QT_X11_NO_MITSHM 1
# - for Python
ENV PYTHONPATH="/opt/ost/stage/lib64/python2.7/site-packages:${PYTHONPATH}"
# - for PATH
ENV PATH="/opt/ost/stage/bin:${PATH}"
# ENVIRONMENT
##############################################################################
ENV OST_ROOT="/usr/local"
ENV OPENSTRUCTURE_VERSION="1.7.1"
ENV PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64"
ENV QT_X11_NO_MITSHM=1
ENTRYPOINT ["ost"]
CMD ["-i"]
docker/README.rst
+ 94
− 21
View file @ 1ddb7ab9
......@@ -9,27 +9,44 @@ OST Docker
Build Docker image
------------------
In order to build OST image:
.. code-block:: bash
cd <OST ROOT>/docker
docker build --tag <TAG> .
cd <PATH TO OST>/docker
docker build --tag <IMAGE NAME> --build-arg OPENSTRUCTURE_VERSION=<VERSION> -f Dockerfile .
One can chose any tag eg. ost.
or if you downloaded the Dockerfile directly:
Run script with OST
-------------------
.. code-block:: bash
In order to run OST script do:
docker build --tag <IMAGE NAME> --build-arg OPENSTRUCTURE_VERSION=<VERSION> -f <DOCKERFILE NAME> <PATH TO DOCKERFILE DIR>
.. code-block:: bash
You can chose any image name (tag) eg. ost. The `OPENSTRUCTURE_VERSION`
build argument is mandatory and image will not built without it. See
`CHANGELOG <https://git.scicore.unibas.ch/schwede/openstructure/blob/master/CHANGELOG.txt>`_
for current list of available releases.
docker run [DOCKER OPTIONS] --rm -v <PATH TO SCRIPT DIR>:/home <IMAGE NAME> /home/<SCRIPT NAME> [SCRIPT OPTIONS]
Testing the image
-----------------
One can find a exemplary script (`test_docker.py`) in the downloaded directory.
To run it do:
.. code-block::
cd <PATH TO OST>/docker
docker run --rm -v $(pwd):/home <IMAGE NAME> test_docker.py
.. warning::
As the last line you should see `OST is working!`.
If script requires some external files eg. PDBs, they have to be located in the
Run script and action with OST
------------------------------
.. note::
If script or action requires some external files eg. PDBs, they have to be located in the
path accessible via mounted volume and should be accessed via docker (NOT LOCAL)
path. Eg. assuming that we have a struc.pdb file in /home/user/pdbs directory and
a script.py in /home/user we could mount the /home/user to /home in docker as
......@@ -45,39 +62,95 @@ In order to run OST script do:
.. code-block:: bash
docker run --rm -v /home/user:/home <IMAGE NAME> home/script.py /home/pdbs/struct.pdb
An easy solution to mount a CWD is to use $(pwd) command in the -v option
of the Docker. For an example see the action exemplary run.
The same reasoning is valid for the output files.
Actions
#######
To see the list of available actions do:
.. code-block::
docker run --rm <IMAGE NAME> -h
To run chosen action do:
One can find a exemplary script (`test_docker.py`) in the <OST ROOT>/docker
directory. To run it do:
.. code-block::
docker run --rm <IMAGE NAME> <ACTION NAME>
Here is an example run of compare-structures action mimicking CAMEO evaluation:
.. code-block::
docker run --rm -v $(pwd):/home <IMAGE NAME> compare-structures \
--model model.pdb \
--reference reference.pdb \
--output output.json \
--qs-score \
--residue-number-alignment \
--lddt \
--structural-checks \
--consistency-checks \
--inclusion-radius 15.0 \
--bond-tolerance 15.0 \
--angle-tolerance 15.0 \
--molck \
--remove oxt hyd unk \
--clean-element-column \
--map-nonstandard-residues
In order to see all available options for this action run:
.. code-block::
cd <OST ROOT>/docker
docker run --rm -v <OST ROOT>/docker:/home <IMAGE NAME> test_docker.py
docker run --rm <IMAGE NAME> compare-structures -h
Scripts
#######
In order to run OST script do:
.. code-block:: bash
docker run [DOCKER OPTIONS] --rm -v <PATH TO SCRIPT DIR>:/home <IMAGE NAME> /home/<SCRIPT NAME> [SCRIPT OPTIONS]
Run script with utility command
Run ost with utility command
###############################
One can also use provided utility bash script `run_docker_ost` to run basic
scripts:
scripts and actions:
.. code-block:: bash
<OST ROOT>/docker/run_docker_ost <IMAGE_NAME> [<SCRIPT_PATH>] [SCRIPT OPTIONS]
<PATH TO OST>/docker/run_docker_ost <IMAGE_NAME> [<SCRIPT_PATH>] [SCRIPT OPTIONS]
One just needs to provide image name and optionally a script and its options. It
is useful to link the command to the binary directory eg. in linux:
One just needs to provide image name and optionally a script/action and its
options. It is useful to link the command to the binary directory eg. in linux:
.. code-block:: bash
ln -s <OST ROOT>/docker/run_docker_ost /usr/bin/run_docker_ost
ln -s <PATH TO OST>/docker/run_docker_ost /usr/bin/run_docker_ost
In order to run an exemplary script (`test_docker.py`) do:
.. code-block::
cd <OST ROOT>/docker
cd <PATH TO OST>/docker
./run_docker_ost <IMAGE NAME> test_docker.py
To see the help for compare-structures action run:
.. code-block::
cd <PATH TO OST>/docker
./run_docker_ost <IMAGE NAME> compare-structures
Run GUI
-------
......
docker/run_docker_ost
+ 10
− 5
View file @ 1ddb7ab9
......@@ -12,12 +12,17 @@ if [[ ${#@} -lt 1 ]]; then
fi
if [[ -z ${script_path} ]]; then
docker run -ti --rm ${image_name}
docker run -ti --rm -v $(pwd):/home ${image_name}
else
abspath=$(readlink -f $script_path)
dirpath=$(dirname $abspath)
name=$(basename $script_path)
docker run --rm -v ${dirpath}:/home ${image_name} /home/${name} ${@:3}
if [[ -e $script_path ]]; then
abspath=$(readlink -f $script_path)
dirpath=$(dirname $abspath)
name=$(basename $script_path)
docker run --rm -v ${dirpath}:/home ${image_name} /home/${name} ${@:3}
else
# it is maybe an action if it does not exist
docker run --rm -v $(pwd):/home ${image_name} ${script_path} ${@:3}
fi
fi
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