Merge branch 'release-3.0.0'

a7fd92d3 · Bienchen · a8c07e87 · 2f89335b · a7fd92d3 · a7fd92d3
Commit a7fd92d3 authored Mar 23, 2020 by Bienchen
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,6 +5,16 @@
 Changelog
 ================================================================================

+Release 3.0.0
+--------------------------------------------------------------------------------
+
+* First release supporting Python 3. Python 2 support has been dropped.
+* Updated versions of dependencies.
+* Reduced amount of warnings during compilation.
+* Improved and simplified use of Docker and Singularity containers.
+* Several minor bug fixes, improvements, and speed-ups.
+
+
 Release 2.1.0
 --------------------------------------------------------------------------------

@@ -15,7 +25,7 @@ Release 2.1.0
  to parametrize arbitrary compounds. 
 * Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
  The algorithm is based on principles of geometric hashing.
-* Several minor bug fixes, improvements, and speed-ups  
+* Several minor bug fixes, improvements, and speed-ups


 Release 2.0.0

--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,7 +6,15 @@
 #    DISABLE_DOCTEST: Don't run example code from documentation on 'make check'
 #    DISABLE_LINKCHECK: Don't test links from documentation on 'make check'
 # (if documentation is disabled, there is no doctest, linkcheck at all)
-cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.10.2 FATAL_ERROR)
+
+# Set CMake policies
+# Behaviour of target_link_libraries, always link by full path. CMP0060 can
+# disable this to stay compatible with old projects. We want the new behaviour
+# since before we needed to provide the full path ourselves, that is: we
+# manually forced CMake to the new scheme.
+cmake_policy(SET CMP0060 NEW)
+
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
 set(CMAKE_EXPORT_COMPILE_COMMANDS 1)

@@ -15,8 +23,8 @@ project(ProMod3 CXX C)
 include(PROMOD3)

 # versioning info
-set(PROMOD3_VERSION_MAJOR 2)
-set(PROMOD3_VERSION_MINOR 1)
+set(PROMOD3_VERSION_MAJOR 3)
+set(PROMOD3_VERSION_MINOR 0)
 set(PROMOD3_VERSION_PATCH 0)
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
 set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
@@ -79,7 +87,7 @@ file(MAKE_DIRECTORY ${STAGE_DIR}
 setup_compiler_flags()

 # Python needed before Boost
-find_package(Python 2.7 REQUIRED)
+find_package(Python 3.6 REQUIRED)
 # Split version string
 string(REPLACE "." ";" _python_version_list ${PYTHON_VERSION})
 list(GET _python_version_list 0 PYTHON_VERSION_MAJOR)
@@ -88,12 +96,12 @@ list(GET _python_version_list 1 PYTHON_VERSION_MINOR)
 setup_boost()

 if(NOT DISABLE_DOCUMENTATION)
-  find_package(Sphinx ${PYTHON_VERSION} REQUIRED)
+  find_package(Sphinx REQUIRED)
  set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
  # this URL should always point to the latest version of OST
  set(OST_DOC_URL "https://www.openstructure.org/docs")
 endif()
-find_package(OPENSTRUCTURE 1.11.0 REQUIRED
+find_package(OPENSTRUCTURE 2.0.0 REQUIRED
             COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)

 if(CMAKE_COMPILER_IS_GNUCXX)

--- a/NOTICE
+++ b/NOTICE
 ProMod3 - A Versatile Homology Modelling Toolbox
-Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
                         Biozentrum - University of Basel

 ProMod3 is developed in the Schwede lab at the Biozentrum - University of Basel. 

--- a/actions/doc/index.rst
+++ b/actions/doc/index.rst
@@ -138,7 +138,7 @@ objects is performed in the
 :class:`~promod3.core.pm3argparse.PM3ArgumentParser` class as described in
 detail :meth:`here <promod3.core.pm3argparse.PM3ArgumentParser.AddFragments>`.

-The default modelling pipeline in ProMod3 is optimized to generate a gap-free 
+The default modelling pipeline in |project| is optimized to generate a gap-free 
 model of the region in the target sequence(s) that is covered with template 
 information. Terminal extensions without template coverage are negelected. 
 You can enforce a model of the full target sequence(s) by adding ``-t``. 

--- a/actions/pm-build-model
+++ b/actions/pm-build-model
-# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
 #                          Biozentrum - University of Basel
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");

--- a/actions/pm-build-rawmodel
+++ b/actions/pm-build-rawmodel
-# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
 #                          Biozentrum - University of Basel
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");

--- a/actions/pm-build-sidechains
+++ b/actions/pm-build-sidechains
-# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
 #                          Biozentrum - University of Basel
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");

--- a/actions/pm-help
+++ b/actions/pm-help
-# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
 #                          Biozentrum - University of Basel
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");

--- a/actions/tests/test_action_build-model.py
+++ b/actions/tests/test_action_build-model.py
-# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
 #                          Biozentrum - University of Basel
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");

--- a/actions/tests/test_action_build-rawmodel.py
+++ b/actions/tests/test_action_build-rawmodel.py
-# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
 #                          Biozentrum - University of Basel
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");

--- a/actions/tests/test_action_help.py
+++ b/actions/tests/test_action_help.py
-# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
 #                          Biozentrum - University of Basel
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");

--- a/actions/tests/test_actions.py
+++ b/actions/tests/test_actions.py
-# Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+# Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
 #                          Biozentrum - University of Basel
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");

--- a/cmake_support/FindPython.cmake
+++ b/cmake_support/FindPython.cmake
@@ -18,8 +18,8 @@
 # Author: Marco Biasini/ Stefan Bienert
 #-------------------------------------------------------------------------------

-set(PYTHON_VERSIONS 2.7)
-set(PYTHON_MIN_VERSION 2.7)
+set(PYTHON_VERSIONS 3.8 3.7 3.6 )
+set(PYTHON_MIN_VERSION 3.6.0)

 #-------------------------------------------------------------------------------
 # check for python framework
@@ -47,6 +47,7 @@ macro(_find_python PYTHON_ROOT VERSION)
  if(PYTHON_ROOT)
    find_library(PYTHON_LIBRARIES
      NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
+      "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
      HINTS "${PYTHON_ROOT}"
      PATH_SUFFIXES lib libs
      NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
@@ -55,16 +56,19 @@ macro(_find_python PYTHON_ROOT VERSION)
      NAMES Python.h
      HINTS "${PYTHON_ROOT}/include"
      PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"
+      "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
      NO_SYSTEM_ENVIRONMENT_PATH NO_DEFAULT_PATH
    )
  else()
    find_library(PYTHON_LIBRARIES
      NAMES "python${_VERSION_NO_DOTS}" "python${VERSION}"
+      "python${_VERSION_NO_DOTS}m" "python${VERSION}m"
      PATH_SUFFIXES lib
    )
    find_path(PYTHON_INCLUDE_PATH
      NAMES Python.h
-      PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"     
+      PATH_SUFFIXES include "python${_VERSION_NO_DOTS}" "python${VERSION}"  
+      "python${_VERSION_NO_DOTS}m" "python${VERSION}m"   
    )    
  endif()  
 endmacro()

--- a/cmake_support/FindSphinx.cmake
+++ b/cmake_support/FindSphinx.cmake
-#-------------------------------------------------------------------------------
-# Check for Sphinx binary
-#
-#    SPHINX_BINARY            is set to the path to the sphinx-build executable,
-#                             preferably sphinx-build-${Sphinx_FIND_VERSION} if
-#                             provided. Also admires PYTHON_ROOT if available.
-#
-# Author: Bienchen
-#-------------------------------------------------------------------------------
+IF(PYTHON_BINARY)
+  EXEC_PROGRAM ("${PYTHON_BINARY}"
+    ARGS "-c 'import sphinx; print(sphinx.__version__)'"
+    OUTPUT_VARIABLE VERSION_STRING
+    RETURN_VALUE SPHINX_NOT_FOUND)
+  if (SPHINX_NOT_FOUND)
+    set(SPHINX_FOUND FALSE)
+  else (SPHINX_NOT_FOUND)
+    set(SPHINX_FOUND TRUE)
+    set(SPHINX_VERSION ${VERSION_STRING})
+  endif (SPHINX_NOT_FOUND)
+ENDIF(PYTHON_BINARY)

-if(Sphinx_FIND_VERSION)
-  set(ADD_SPHINX_NAMES "sphinx-build-${Sphinx_FIND_VERSION}")
-endif()
+if (SPHINX_FOUND)
+  message(STATUS "Sphinx version: " ${SPHINX_VERSION})
+else (SPHINX_FOUND)
+  if (Sphinx_FIND_REQUIRED)
+    message (FATAL_ERROR "Could not import sphinx in " ${PYTHON_BINARY}
+             " make it available or disable documentation with -DDISABLE_DOCUMENTATION")
+  endif (Sphinx_FIND_REQUIRED)
+endif (SPHINX_FOUND)

-if(PYTHON_ROOT)
-  find_program(SPHINX_BINARY NAMES sphinx-build ${ADD_SPHINX_NAMES}
-    HINTS ${PYTHON_ROOT}
-    PATH_SUFFIXES bin
-    DOC "Sphinx documentation generator"
-  )
-else()
-  find_program(SPHINX_BINARY NAMES sphinx-build ${ADD_SPHINX_NAMES}
-    PATH_SUFFIXES bin
-    DOC "Sphinx documentation generator"
-  )
-endif()
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(Sphinx DEFAULT_MSG
-  SPHINX_BINARY
-)
-
-mark_as_advanced(
-  SPHINX_BINARY
-)
--- a/cmake_support/PROMOD3.cmake
+++ b/cmake_support/PROMOD3.cmake
@@ -1019,10 +1019,10 @@ macro(setup_boost)
  #              python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR} REQUIRED)
  # set(BOOST_PYTHON_LIBRARIES ${Boost_LIBRARIES})
  # see https://cmake.org/cmake/help/v3.11/module/FindBoost.html
-  foreach(_python_lib_name python
-                           python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}
+  foreach(_python_lib_name python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}
                           python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
-                           python${PYTHON_VERSION_MAJOR})
+                           python${PYTHON_VERSION_MAJOR}
+                           python)
    find_package(Boost ${_BOOST_MIN_VERSION} COMPONENTS ${_python_lib_name} QUIET)
    if(Boost_FOUND)
      message(STATUS "Found Boost package: " ${_python_lib_name})

--- a/config/src/config.hh.in
+++ b/config/src/config.hh.in
-// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and 
+// Copyright (c) 2013-2020, SIB - Swiss Institute of Bioinformatics and
 //                          Biozentrum - University of Basel
 // 
 // Licensed under the Apache License, Version 2.0 (the "License");

--- a/container/Dockerfile
+++ b/container/Dockerfile
-FROM ubuntu:18.04
+ARG OPENSTRUCTURE_VERSION="2.0.0"
+FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_VERSION}

 # ARGUMENTS
 ###########
-ARG OPENSTRUCTURE_VERSION="1.11.0"
-ARG PROMOD_VERSION="2.1.0"
+ARG PROMOD_VERSION="3.0.0"
 ARG SRC_FOLDER="/usr/local/src"
-ARG CPUS_FOR_MAKE=4
-ARG COMPLIB_DIR="/usr/local/share/ost_complib"
-ARG OPENMM_VERSION="7.1.1"
-ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/"
-ARG OPENMM_LIB_PATH="/usr/local/openmm/lib/"

-ENV DEBIAN_FRONTEND=noninteractive
-
-# INSTALL SYSTEM DEPS
-#####################
-RUN apt-get update -y && apt-get install -y cmake \
-                                            g++ \
-                                            sip-dev \
-                                            libtiff-dev \
-                                            libfftw3-dev \
-                                            libeigen3-dev \
-                                            libboost-all-dev \
-                                            libpng-dev \
-                                            python2.7 \
-                                            python-pyqt5 \
-                                            qt5-qmake \
-                                            qtbase5-dev \
-                                            python-qt4 \
-                                            python-numpy \
-                                            python-scipy \
-                                            python-pandas \
-                                            python-matplotlib \
-                                            wget \
-                                            gfortran \
-                                            python-pip \
-                                            python-sphinx \
-                                            tar \
-                                            libbz2-dev \
-                                            doxygen \
-                                            swig \
-                                            clustalw \
-                                            libsqlite3-dev \
-                                            dssp \
-                                            python-enum34 \
-                                            locales && \
-                      # CLEANUP
-                      rm -rf /var/lib/apt/lists/*
-
-# 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

 # ENVIRONMENT
 ##############################################################################
-ENV OPENSTRUCTURE_VERSION="${OPENSTRUCTURE_VERSION}"
 ENV PROMOD_VERSION="${PROMOD_VERSION}"
-ENV OST_ROOT="/usr/local"
-ENV DNG_ROOT="/usr/local"
 ENV PROMOD_ROOT="/usr/local"
-ENV PYTHONPATH="/usr/local/lib64/python2.7/site-packages:${PYTHONPATH}"
-ENV LD_LIBRARY_PATH="/usr/local/lib64:/usr/local/openmm/lib/$LD_LIBRARY_PATH"
-ENV QT_X11_NO_MITSHM=1

-# 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 && \
-    cd ${SRC_FOLDER} && rm ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
-    rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
-
-# INSTALL OST
-#############
-RUN cd ${SRC_FOLDER} && \
-    # copy ost release
-    wget -O openstructure-${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 \
-             -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 && \
-    make -j ${CPUS_FOR_MAKE} &&\
-    # 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 $COMPLIB_DIR && chmod a+rw -R $COMPLIB_DIR && mv compounds.chemlib $COMPLIB_DIR && \
-    # rerun cmake and specify compound lib location
-    cmake .. -DCOMPOUND_LIB=$COMPLIB_DIR/compounds.chemlib && \
-    # Build OST with compound library
-    make -j ${CPUS_FOR_MAKE} && make check && make install && \
-    # cleanup
-    cd ${SRC_FOLDER} && rm ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}.tar.gz && \
-    rm -rf ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} && \
-    # BEND AROUND COMPOUND LIB
-    # By default, the compound library is moved to 
-    # /usr/local/share/openstructure/compounds.chemlib upon building
-    # We replace that file with a symbolic link to the compound.chemlib in
-    # $COMPLIB_DIR
-    # The advantage is that we can later on mount any directory containing this file
-    # in that directory and override the compound lib with updated versions.
-    rm /usr/local/share/openstructure/compounds.chemlib && \
-    ln -s $COMPLIB_DIR/compounds.chemlib /usr/local/share/openstructure/compounds.chemlib

 # INSTALL ProMod3
 #################
@@ -132,13 +24,15 @@ RUN cd ${SRC_FOLDER} && \
    cd ${SRC_FOLDER}/promod-${PROMOD_VERSION}/build && \
    # Build and install ProMod3
    cmake .. -DOST_ROOT=/usr/local \
-             -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython2.7.so \
-             -DOPTIMIZE=ON \
-             -DENABLE_SSE=1 && \
-    make -j ${CPUS_FOR_MAKE} && make codetest && make doctest && \
-    make install && \
+             -DPYTHON_LIBRARIES=/usr/lib/x86_64-linux-gnu/libpython3.6m.so \
+             -DOPTIMIZE=1 \
+             -DENABLE_SSE=1 \
+             -DDISABLE_DOCUMENTATION=1 && \
+ 
+    make && make check && make install && \
    # cleanup
    cd ${SRC_FOLDER} && rm ${SRC_FOLDER}/promod-${PROMOD_VERSION}.tar.gz && \
    rm -rf ${SRC_FOLDER}/promod-${PROMOD_VERSION}

-WORKDIR /home
+ENTRYPOINT ["pm"]
+
--- a/container/Singularity
+++ b/container/Singularity
 BootStrap: docker
-Registry: http://localhost:5000
-Namespace:
-From: promod:latest
-
+From: registry.scicore.unibas.ch/schwede/promod3:3.0.0
 %post
 ##############################################################################
 # POST
 ##############################################################################

+
 # CHANGE DASH TO BASH
 rm /bin/sh
 ln -sf /bin/bash /bin/sh

-# INSTALL NGL AND JUPYTER WITH PIP
-######################################
-pip install --no-cache-dir nglview==1.1.6 \
-                           jupyter==1.0.0

-# SETUP JUPYTER
-###############
+# INSTALL SYSTEM DEPS
+#####################
+apt-get update -y && apt-get install -y python3-pip
+pip3 install nglview \
+             ipython \
+             jupyter 
+
+# SETUP IPYTHON / JUPYTER
+#########################
+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="/tmp/jupyter_runtime"
 mkdir -p /usr/local/share/ipython
-mkdir -p /usr/local/share/jupyter
-mkdir -p /usr/local/etc/jupyter
-mkdir -p /usr/local/share/jupyter/runtime
-mkdir -p /usr/local/share/jupyter/kernels/ost-kernel
+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 /usr/local/share/jupyter
-chmod a+rw -R /usr/local/etc/jupyter
-chmod a+rw -R /usr/local/share/jupyter/runtime
-cat > /usr/local/share/jupyter/kernels/ost-kernel/kernel.json <<EOF
+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",
+  "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

@@ -50,11 +55,181 @@ jupyter nbextension enable nglview --py --sys-prefix
 ##############################################################################
 # ENVIRONMENT
 ##############################################################################
-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 TEMP="/tmp"
+export TEMPDIR="/tmp"
+export TMPDIR="/tmp"
+export TMP="/tmp"
+# As the Singularity mounts $HOME by default Jupyter and Ipython config files
+# are moved to separate directories. Proper environmental variables are also 
+# set
+export IPYTHONDIR="/usr/local/share/ipython"
+export JUPYTER_CONFIG_DIR="/usr/local/etc/jupyter"
+export JUPYTER_PATH="/usr/local/share/jupyter"
+export JUPYTER_RUNTIME_DIR="$TMPDIR/jupyter_runtime"
+
+
+%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 the OpenStructure executable and can be used to run an 
+interactive shell, scripts and OpenStructure actions. 
+ProMod3 modules can be imported as any other Python module.
+
+Usage:
+    singularity run --app OST <IMAGE> [options] (script | action)
+    [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]
+
+To list all available actions:
+    singularity run --app OST <IMAGE> --help
+
+If script requires some external files eg. PDBs, they have to be located in the
+path accessible via mounted volumes. By default Singularity mounts $HOME and
+goes to CWD. Thus this sould work as expected out of the box.
+
+
+%apprun PM
+##############################################################################
+# PM APP
+##############################################################################
+$PROMOD_ROOT/bin/pm "$@"
+
+%apphelp PM
+The PM app exposes the ProMod3 executable and can be used to run scripts and
+predefined modelling "actions".
+
+Usage:
+    singularity run --app PM <IMAGE> [options] (script | action)
+    [parameters]
+
+Options:
+    -h, --help            show this help message and exit
+    -v VLEVEL, --verbosity_level=VLEVEL
+                          sets the verbosity level [default: 2]
+
+To list all available actions:
+    singularity run --app PM <IMAGE> help
+
+
+If script/action requires some external files eg. PDBs, they have to be located