From 60dcf524bb33ba7c11eae537ab95b670bf6afc64 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 9 Dec 2019 16:52:19 +0100
Subject: [PATCH] Python 3 Singularity Container
biggest change: make it rely on ost docker-container as base image
---
singularity/Singularity | 236 ++++++++--------------------------------
1 file changed, 45 insertions(+), 191 deletions(-)
diff --git a/singularity/Singularity b/singularity/Singularity
index 429cb86a5..ea57eab41 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -1,170 +1,38 @@
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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