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Commit 35c3954a authored by Gerardo Tauriello's avatar Gerardo Tauriello
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SCHWED-4329: Stop overcomplicating Singularity recipe naming.

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......@@ -9,7 +9,7 @@ In order to build OST Singularity image:
.. code-block:: bash
cd <OST ROOT>/singularity
sudo singularity build ost.img Singularity.1.9.0
sudo singularity build ost.img Singularity
.. note::
......
singularity/Singularity.1.10.0 → singularity/Singularity
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BootStrap: docker
From: ubuntu:16.04
%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:${PYTHONPATH}"
# When changing OPENSTRUCTURE_VERSION make sure to change it also in the
# environment section of singularity recipe (this file).
export OPENSTRUCTURE_VERSION="1.9.0"
export OPENSTRUCTURE_SHARE="/usr/local/share/ost"
export MSMS_VERSION="2.6.1"
export OPENMM_VERSION="7.1.1"
export DSSP_VERSION="2.2.1"
export OPENMM_INCLUDE_PATH=/usr/local/openmm/include/
export OPENMM_LIB_PATH=/usr/local/openmm/lib/
export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
export JUPYTER_PATH="/usr/local/share/jupyter"
export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
export VIRTUALENV_DIR="/usr/local/share/ost_venv"
# INSTALL SYSTEM DEPS
#####################
apt-get update -y && apt-get install -y cmake \
sip-dev \
libtiff-dev \
libfftw3-dev \
libeigen3-dev \
libboost-all-dev \
libpng-dev \
python-all \
python2.7 \
python-qt4 \
qt4-qtconfig \
qt4-qmake \
libqt4-dev \
libpng-dev \
wget \
git \
gfortran \
python-pip \
tar \
libbz2-dev \
doxygen \
swig \
clustalw \
python-virtualenv \
libsqlite3-dev \
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
# SET UP VIRTUALENV
###################
virtualenv --system-site-packages $VIRTUALENV_DIR
. $VIRTUALENV_DIR/bin/activate
# 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
# COMPILE AND INSTALL DSSP
##############
cd ${SRC_FOLDER}
if [ ! -f dssp-${DSSP_VERSION}.tgz ]; then
wget ftp://ftp.cmbi.umcn.nl/pub/molbio/software/dssp-2/dssp-${DSSP_VERSION}.tgz
tar -xvzf dssp-${DSSP_VERSION}.tgz
cd dssp-${DSSP_VERSION}
make -j ${CPUS_FOR_MAKE}
make 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
###############
mkdir -p /usr/local/share/ipython
mkdir -p $JUPYTER_PATH
mkdir -p $JUPYTER_RUNTIME_DIR
mkdir -p $JUPYTER_CONFIG_DIR
mkdir -p $JUPYTER_PATH/kernels/ost-kernel
chmod a+rw -R /usr/local/share/ipython
chmod a+rw -R $JUPYTER_PATH
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",
"-f", "{connection_file}",
"--InteractiveShellApp.exec_PYTHONSTARTUP=False",
"--InteractiveShellApp.exec_files=['/usr/local/lib64/python2.7/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 $SRC_FOLDER/*
cd /home
%environment
##############################################################################
# ENVIRONMENT
##############################################################################
export OST_ROOT="/usr/local"
export OPENSTRUCTURE_VERSION="1.9.0"
export OPENMM_LIB_PATH=/usr/local/openmm/lib/
export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64:${OPENMM_LIB_PATH}"
export QT_X11_NO_MITSHM=1
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 VIRTUALENV_DIR="/usr/local/share/ost_venv"
%apprun ChemdictTool
##############################################################################
# CHEMDICT TOOL APP
##############################################################################
$OST_ROOT/bin/chemdict_tool "$@"
%apprun lDDT
##############################################################################
# lDDT APP
##############################################################################
$OST_ROOT/bin/lddt "$@"
%apphelp lDDT
The Local Distance Difference Test.
Usage:
singularity run --app lDDT <IMAGE> [options] <mod1> [mod1 [mod2]] <re1>[,ref2,ref3]
Options:
-s selection performed on ref
-c use Calphas only
-f perform structural checks and filter input data
-t fault tolerant parsing
-p <file> use specified parmeter file. Mandatory
-v <level> verbosity level (0=results only,1=problems reported, 2=full report)
-b <value> tolerance in stddevs for bonds
-a <value> tolerance in stddevs for angles
-r <value> distance inclusion radius
-i <value> sequence separation
-e print version
-x ignore residue name consistency checks
%apprun Molck
##############################################################################
# MOLCK APP
##############################################################################
$OST_ROOT/bin/molck "$@"
%apphelp Molck
This is molck - the molecule checker
Usage:
singularity run --app Molck <IMAGE> [options] file1.pdb [file2.pdb [...]]
Options:
--complib=path location of the compound library file. If not provided, the
following locations are searched in this order:
1. Working directory, 2. OpenStructure standard library location (if the
executable is part of a standard OpenStructure installation)
--rm=<a>,<b> remove atoms and residues matching some criteria
zeroocc - Remove atoms with zero occupancy
hyd - Remove hydrogen atoms
oxt - Remove terminal oxygens
nonstd - Remove all residues not one of the 20 standard amino acids
unk - Remove unknown and atoms not following the nomenclature
--fix-ele clean up element column
--stdout write cleaned file(s) to stdout
--out=filename write cleaned file(s) to disk. % characters in the filename are
replaced with the basename of the input file without extension.
Default: %-molcked.pdb
--color=auto|on|off
whether output should be colored
--map-nonstd maps modified residues back to the parent amino acid, for example
MSE -> MET, SEP -> SER.
%apprun OST
##############################################################################
# OST APP
##############################################################################
$OST_ROOT/bin/ost "$@"
%apphelp OST
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]
Options:
-i, --interactive start interpreter interactively (must be first
parameter, ignored otherwise)
-h, --help show this help message and exit
-v VLEVEL, --verbosity_level=VLEVEL
sets the verbosity level [default: 2]
If script requires some external files eg. PDBs, they have to be located in the
path accessible via mounted volumes. By default Singularity mounts $HOME and
goes to CWD. Thus this sould work as expected out of the box.
%appenv IPython
##############################################################################
# NOTEBOOK ENV
##############################################################################
export DNG_ROOT=$OST_ROOT
export DNG_INITDIR=${DNG_ROOT}/lib64/python2.7/site-packages/ost
%apprun IPython
##############################################################################
# OST IPYTON APP
##############################################################################
. $VIRTUALENV_DIR/bin/activate && ipython -i $DNG_INITDIR/ost_startup.py "$@"
%apphelp IPython
OST-powered iPython shell.
Usage:
singularity run --app IPython <IMAGE> [options]
Detailed help:
singularity run --app IPython <IMAGE> --help
%appenv Notebook
##############################################################################
# NOTEBOOK ENV
##############################################################################
export BIN_DIR=$OST_ROOT/bin
export XDG_RUNTIME_DIR=""
. $OST_ROOT/libexec/openstructure/ost_config
%apprun Notebook
##############################################################################
# NOTEBOOK APP
##############################################################################
. $VIRTUALENV_DIR/bin/activate && jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@"
%apphelp Notebook
A Jupyter notebook palyground with OST and nglview.
Usage:
singularity run --app Notebook <IMAGE> [options]
The Jupyter notebook is run by default with `--NotebookApp.iopub_data_rate_limit=10000000`
and `--no-browser` options.
Useful options when running on remote server:
--ip=<Unicode> (NotebookApp.ip)
Default: 'localhost'
The IP address the notebook server will listen on.
--port=<Integer> (NotebookApp.port)
Default: 8888
The port the notebook server will listen on.
Copy the URL to the browser and launch the notebook with OST kernel. This will
load all necessary OST components just like in the OST shell. We also enabled
the nglview widget to interactively view molecular structures and trajectories.
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.
To list of all available options:
singularity run --app Notebook <IMAGE> --help
%runscript
##############################################################################
# RUNSCRIPT
##############################################################################
cat << EOF
Singularity container for OST $OPENSTRUCTURE_VERSION.
This container includes the following apps:
* OST - OpenStructure binary
* IPython - OST-powered iPython shell
* Notebook - A Jupyter notebook palyground with OST and nglview
* lDDT - The Local Distance Difference Test
* Molck - Molecular checker
* ChemdictTool - Creating or update a compound library
To see the help for each individual app run:
singularity help --app <APP NAME> <IMAGE NAME>
EOF
%help
Singularity container for OST.
This container includes the following apps:
* OST - OpenStructure binary
* IPython - OST-powered iPython shell
* Notebook - A Jupyter notebook palyground with OST and nglview
* lDDT - The Local Distance Difference Test
* Molck - Molecular checker
* ChemdictTool - Creating or update a compound library
To see the help for each individual app run:
singularity help --app <APP NAME> <IMAGE NAME>
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