feat: SCHWED-3097 Add Singularity definition file

singularity/README.rst

+OST Singularity
+===============
+
+.. note::
+
+  In order to run some singularity commands there might be a need to run them as root (sudo).
+
+Build Singularity image
+------------------
+
+In order to build OST Singularity image:
+
+.. code-block:: bash
+
+  cd <OST ROOT>/singularity
+  singularity build ost.img Singularity.1.7.1
+
+One can chose any name for an image. For the purose of this file we will assume
+that the image name is `ost.img`.
+
+Run script using OST
+--------------------
+
+In order to run OST script do:
+
+.. code-block:: bash
+  singularity run --app OST ost.img <SCRIPT NAME> [SCRIPT OPTIONS]
+
+.. warning::
+
+  If script requires some external files eg. PDBs, they have to be located in the
+  path accessible via mounted volume. By default Singularity mounts $HOME and
+  goes to CWD. Thus this sould work as expected.
+
+One can find a exemplary script (`test_docker.py`) in the <OST ROOT>/docker
+directory. To run it do:
+
+.. code-block::
+
+  cd <OST ROOT>/singularity
+  singularity run --app OST ost.img ../docker/test_docker.py
+
+Available apps
+--------------
+
+TODO

singularity/Singularity.1.7.1

+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:${PYTHONPATH}"
+export OPENSTRUCTURE_VERSION="1.7.1"
+export OPENSTRUCTURE_SHARE="/usr/local/share/ost"
+export MSMS_VERSION="2.6.1"
+export OPENMM_VERSION="7.1.1"
+export DSSP_VERSION="2.2.1"
+export OPENMM_INCLUDE_PATH=/usr/local/openmm/include/
+export OPENMM_LIB_PATH=/usr/local/openmm/lib/
+export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
+export JUPYTER_PATH="/usr/local/share/jupyter"
+export JUPYTER_RUNTIME_DIR="$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
+
+# SET UP VIRTUALENV
+###################
+virtualenv --system-site-packages $VIRTUALENV_DIR
+. $VIRTUALENV_DIR/bin/activate
+
+
+# INSTALL REQUIRED PYTHON PACKAGES
+##################################
+pip install --upgrade pip && pip install numpy==1.10.4 \
+                                         scipy==1.0.0 \
+                                         pandas==0.22.0 \
+                                         jupyter==1.0.0 \
+                                         nglview==1.0
+
+# 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.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
+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 > $JUPYTER_PATH/kernels/ost-kernel/kernel.json <<EOF
+{
+	"display_name": "OST",
+	"language": "python",
+	"argv": [
+		"python",
+		"-m", "ipykernel",
+        "-f", "{connection_file}",
+		"--InteractiveShellApp.exec_PYTHONSTARTUP=False",
+		"--InteractiveShellApp.exec_files=['/usr/local/lib64/python2.7/site-packages/ost/ost_startup.py']"
+	],
+	"env": {
+	}
+}
+EOF
+
+jupyter nbextension enable nglview --py --sys-prefix
+
+# GO HOME
+#########
+
+cd /home
+
+%environment
+##############################################################################
+# ENVIRONMENT
+##############################################################################
+export OST_ROOT="/usr/local"
+export PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
+export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64"
+export QT_X11_NO_MITSHM=1
+export IPYTHONDIR="/usr/local/share/ipython"
+export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
+export JUPYTER_PATH="/usr/local/share/jupyter"
+export JUPYTER_RUNTIME_DIR="$JUPYTER_PATH/runtime"
+export VIRTUALENV_DIR="/usr/local/share/ost_venv"
+
+%apprun ChemdictTool
+##############################################################################
+# CHEMDICT TOOL APP
+##############################################################################
+. $VIRTUALENV_DIR/bin/activate && $OST_ROOT/bin/chemdict_tool "$@"
+
+%apprun lDDT
+##############################################################################
+# lDDT APP
+##############################################################################
+. $VIRTUALENV_DIR/bin/activate && $OST_ROOT/bin/lddt "$@"
+
+%apprun Molck
+##############################################################################
+# MOLCK APP
+##############################################################################
+. $VIRTUALENV_DIR/bin/activate && $OST_ROOT/bin/molck "$@"
+
+%apprun OST
+##############################################################################
+# OST APP
+##############################################################################
+$OST_ROOT/bin/ost "$@"
+
+%appenv Notebook
+##############################################################################
+# NOTEBOOK ENV
+##############################################################################
+export BIN_DIR=$OST_ROOT/bin
+export XDG_RUNTIME_DIR=""
+. $OST_ROOT/libexec/openstructure/ost_config
+
+%apprun Notebook
+##############################################################################
+# NOTEBOOK APP
+##############################################################################
+. $VIRTUALENV_DIR/bin/activate && jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 --no-browser "$@"
+
+%runscript
+##############################################################################
+# RUNSCRIPT
+##############################################################################
+cat << EOF
+Singularity container for OST $OPENSTRUCTURE_VERSION.
+
+This container includes the following apps:
+ * OST - OpenStructure binary
+ * lDDT - The Local Distance Difference Test
+ * Molck - Molecular checker
+ * Notebook - A Jupyter notebook palyground with OST and nglview
+
+To see the help for each individual app run:
+
+   $ singularity run --app APP
+
+
+EOF
+
+

[Gerardo Tauriello]

Should be "playground" Btw: sublime has a built-in spell checker (View/Spell Check). I advice to use it on any text that should be English... ;-)