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Commit 60dcf524 authored by Studer Gabriel's avatar Studer Gabriel
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Python 3 Singularity Container 

biggest change: make it rely on ost docker-container as base image
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singularity/Singularity
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BootStrap: docker
From: ubuntu:18.04
From: registry.scicore.unibas.ch/schwede/openstructure:python3_test
%post
##############################################################################
# POST
##############################################################################
# CHANGE DASH TO BASH
rm /bin/sh
ln -sf /bin/bash /bin/sh
# DEFINE SOME ENV VARS USED DURING THE IMAGE BUILD
##########################
export SRC_FOLDER="/usr/local/src"
export CPUS_FOR_MAKE=8
export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
# When changing OPENSTRUCTURE_VERSION make sure to change it also in the
# environment section of singularity recipe (this file).
export OPENSTRUCTURE_VERSION="1.10.0"
export OPENSTRUCTURE_SHARE="/usr/local/share/ost"
export MSMS_VERSION="2.6.1"
export OPENMM_VERSION="7.1.1"
export OPENMM_INCLUDE_PATH=/usr/local/openmm/include/
export OPENMM_LIB_PATH=/usr/local/openmm/lib/
export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
export VIRTUALENV_DIR="/usr/local/share/ost_venv"
# INSTALL SYSTEM DEPS
#####################
apt-get update -y && apt-get install -y cmake \
g++ \
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 \
doxygen \
swig \
clustalw \
python-virtualenv \
libsqlite3-dev \
dssp \
python-enum34 \
python-ipaddress \
locales
# SET LOCALE
############
echo "LC_ALL=en_US.UTF-8" >> /etc/environment
echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
echo "LANG=en_US.UTF-8" > /etc/locale.conf
locale-gen en_US.UTF-8
# INSTALL SOME PYTHON PACKAGES GLOBALY
######################################
pip install --no-cache-dir numpy==1.10.4 \
scipy==1.0.0 \
pandas==0.22.0
apt-get update -y && apt-get install -y python3-pip \
python3-venv
# SET UP VIRTUALENV
###################
virtualenv --system-site-packages $VIRTUALENV_DIR
export VIRTUALENV_DIR="/usr/local/share/ost_venv"
python3 -m venv --system-site-packages $VIRTUALENV_DIR
. $VIRTUALENV_DIR/bin/activate
pip3 install nglview \
ipython \
jupyter
# INSTALL REQUIRED PYTHON PACKAGES
##################################
pip install jupyter==1.0.0 \
nglview==1.1.6
# DOWNLOAD AND INSTALL MSMS
##############
cd ${SRC_FOLDER}
if [ ! -f msms_i86_64Linux2_${MSMS_VERSION}.tar.gz ]; then
mkdir -p msms
cd 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
fi
# COMPILE OPENMM FROM SOURCES. INSTALL TO /usr/local
############################
cd ${SRC_FOLDER}
if [ ! -f openmm-${OPENMM_VERSION}.tar.gz ]; then
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
fi
# INSTALL OST
#############
cd ${SRC_FOLDER}
if [ ! -f openstructure-${OPENSTRUCTURE_VERSION}.tar.gz ]; then
# 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 && cd ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build
# cmake ost
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
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 $OPENSTRUCTURE_SHARE
# Build and install OST
cmake .. -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
-DOPTIMIZE=ON \
-DENABLE_MM=ON \
-DCOMPILE_TMTOOLS=1 \
-DUSE_NUMPY=1 \
-DOPEN_MM_LIBRARY=$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 chemdict_tool
make -j ${CPUS_FOR_MAKE}
make check
make install
fi
# SETUP JUPYTER
###############
# SETUP IPYTHON / JUPYTER
#########################
export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
mkdir -p /usr/local/share/ipython
mkdir -p $JUPYTER_PATH
mkdir -p $JUPYTER_RUNTIME_DIR
......@@ -176,61 +44,43 @@ chmod a+rw -R $JUPYTER_CONFIG_DIR
chmod a+rw -R $JUPYTER_RUNTIME_DIR
cat > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
{
"display_name": "OST",
"language": "python",
"argv": [
"python",
"-m", "ipykernel",
"display_name": "OST",
"language": "python",
"argv": [
"python",
"-m", "ipykernel",
"-f", "{connection_file}",
"--InteractiveShellApp.exec_PYTHONSTARTUP=False",
"--InteractiveShellApp.exec_files=['/usr/local/lib64/python2.7/site-packages/ost/ost_startup.py']"
],
"env": {
}
"--InteractiveShellApp.exec_PYTHONSTARTUP=False",
"--InteractiveShellApp.exec_files=['/usr/local/lib64/python3.6/site-packages/ost/ost_startup.py']"
],
"env": {
}
}
EOF
jupyter nbextension enable nglview --py --sys-prefix
# GO HOME AND CLEANUP
#####################
apt-get purge -y cmake \
wget \
git \
gfortran \
python-pip \
libbz2-dev \
doxygen \
swig
apt-get clean
apt-get autoremove -y
cd $SRC_FOLDER && rm -rf $SRC_FOLDER/*
cd /home
%environment
##############################################################################
# ENVIRONMENT
##############################################################################
export OST_ROOT="/usr/local"
export OPENSTRUCTURE_VERSION="1.10.0"
export OPENMM_LIB_PATH=/usr/local/openmm/lib/
export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:${OPENMM_LIB_PATH}"
export QT_X11_NO_MITSHM=1
# As the Singularity mounts $HOME by default Jupyter and Ipython config files
# are moved to separate directories. Proper environmental variables are also
# set
export IPYTHONDIR="/usr/local/share/ipython"
export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
export JUPYTER_RUNTIME_DIR="/usr/local/share/jupyter/runtime"
export VIRTUALENV_DIR="/usr/local/share/ost_venv"
%apprun ChemdictTool
##############################################################################
# CHEMDICT TOOL APP
##############################################################################
$OST_ROOT/bin/chemdict_tool "$@"
%apprun lDDT
##############################################################################
# lDDT APP
......@@ -258,6 +108,7 @@ Options:
-e print version
-x ignore residue name consistency checks
%apprun Molck
##############################################################################
# MOLCK APP
......@@ -291,6 +142,7 @@ Options:
--map-nonstd maps modified residues back to the parent amino acid, for example
MSE -> MET, SEP -> SER.
%apprun OST
##############################################################################
# OST APP
......@@ -298,11 +150,12 @@ Options:
$OST_ROOT/bin/ost "$@"
%apphelp OST
The OST app exposes OpenStructure binary and can be used to run interactive shell
and scripts.
The OST app exposes OpenStructure binary and can be used to run interactive
shell and scripts.
Usage:
singularity run --app OST <IMAGE> [ost options] [script to execute] [script parameters]
singularity run --app OST <IMAGE> [ost options] [script to execute]
[script parameters]
Options:
-i, --interactive start interpreter interactively (must be first
......@@ -321,13 +174,14 @@ goes to CWD. Thus this sould work as expected out of the box.
# NOTEBOOK ENV
##############################################################################
export DNG_ROOT=$OST_ROOT
export DNG_INITDIR=${DNG_ROOT}/lib64/python2.7/site-packages/ost
export DNG_INITDIR=${DNG_ROOT}/lib64/python3.6/site-packages/ost
%apprun IPython
##############################################################################
# OST IPYTON APP
##############################################################################
. $VIRTUALENV_DIR/bin/activate && ipython -i $DNG_INITDIR/ost_startup.py "$@"
. $VIRTUALENV_DIR/bin/activate && ipython3 -i $DNG_INITDIR/ost_startup.py "$@"
%apphelp IPython
OST-powered iPython shell.
......@@ -340,6 +194,7 @@ Detailed help:
singularity run --app IPython <IMAGE> --help
%appenv Notebook
##############################################################################
# NOTEBOOK ENV
......@@ -348,6 +203,7 @@ export BIN_DIR=$OST_ROOT/bin
export XDG_RUNTIME_DIR=""
. $OST_ROOT/libexec/openstructure/ost_config
%apprun Notebook
##############################################################################
# NOTEBOOK APP
......@@ -355,7 +211,7 @@ export XDG_RUNTIME_DIR=""
. $VIRTUALENV_DIR/bin/activate && jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@"
%apphelp Notebook
A Jupyter notebook palyground with OST and nglview.
A Jupyter notebook playground with OST and nglview.
Usage:
......@@ -379,8 +235,8 @@ For more details on how to use nglview see http://nglviewer.org/nglview/latest/.
As the Singularity mounts $HOME by default Jupyter and Ipython config files
are moved to separate directories. Proper environmental variables are also set.
In addition, Jupyter is run in a separate virtualenv to not interact with possibly
installed host version.
In addition, Jupyter is run in a separate virtualenv to not interact with
possibly installed host version.
To list of all available options:
......@@ -421,5 +277,3 @@ This container includes the following apps:
To see the help for each individual app run:
singularity help --app <APP NAME> <IMAGE NAME>
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