Singularity.jupyter3ec

# BootStrap: localimage
# From: jupyter23
Bootstrap: shub
From: MBlaschek/singularity-jupyter:jupyter23

%help
	Container Centos 6.10 (docker)
	Glibc: 2.12-1.212.el6.x86_64
	Installed: wget, git, curl, bzip2 ca-certificates
	
	Run a jupyter notebook-server/shell in a container
	Usually: http://localhost:8888
	Anaconda Python 3 (plus kernel 2.7)
	ECMWF eccodes (v2.10, py2/3) + cfgrib (py3)

%post    
	# Install jupyter notebook
	/opt/conda/bin/pip install cfgrib
	# Additonal
	apt-get update
	apt-get install -y --no-install-recommends git build-essential gfortran cmake autotools-dev autoconf libnetcdf*

	# Clean
	apt-get autoremove -y
	apt-get clean

	# Add SRVX8 directories
	mkdir -p /raid8/srvx1
	mkdir -p /opt/dev
	# Add ECMWF Software
	
	# required for CMAKE
	export PATH=/opt/conda/bin:$PATH
	export LD_LIBRARY_PATH=/opt/conda/lib:$LD_LIBRARY_PATH
	
	mkdir /opt/build
	cd /opt/build

	wget https://confluence.ecmwf.int/download/attachments/45757960/eccodes-2.12.0-Source.tar.gz
	wget http://download.ecmwf.org/test-data/eccodes/eccodes_test_data.tar.gz
	tar -xzf eccodes-2.*-Source.tar.gz
	cd eccodes*/
	mkdir build ; cd build
	tar -xzf ../../eccodes_test_data.tar.gz -C .
	cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..
	make -j4 && ctest && make install
	# Clean up build environment
	cd /opt/build
	# preserve for uninstall or further changes
	tar czf eccodes-build.tar.gz eccodes*/
	rm -rf eccodes*/
	# Add Eccodes to Python Path
	echo "/usr/local/lib/python3.7/site-packages" > /opt/conda/lib/python3.7/site-packages/eccodes.pth


%environment
	# important part otherwise the server will try to access /run/user and fail
	export JUPYTER_RUNTIME_DIR=$PWD/.runtime
	# Make sure we use container kernels
	export JUPYTER_DATA_DIR=$PWD/.kernels
	# Development
	export LD_LIBRARY_PATH=/opt/conda/lib:/usr/local/lib:$LD_LIBRARY_PATH