Singularity.faststructure

# Author: B. Anderson
# Singularity recipe for creating a container for using the program fastStructure

Bootstrap: docker
From: ubuntu:18.04

%labels
	MAINTAINER bmichanderson
	PROGRAM fastStructure
	VERSION 1.0

%post
	# update packages and install tools for building
	apt update && apt upgrade -y && apt install -y autoconf automake build-essential git make wget python-pip

	# install dependencies
		# install packages
		pip install numpy==1.16.5 scipy==1.2.1 cython==0.27.3

		# get GNU Scientific Library
		wget https://mirror.ibcp.fr/pub/gnu/gsl/gsl-1.16.tar.gz
		tar -zxvf gsl-1.16.tar.gz
		cd gsl-1.16
		./configure
		make
		make check
		make install
		cd ..
		rm -r gsl-*

	# clean-up
	apt update && apt upgrade -y &&	apt autoremove -y && apt clean

	# install fastStructure
		# get code
		git clone https://github.com/rajanil/fastStructure
		cd fastStructure
		git fetch && git merge origin/master

		# build extensions
		cd vars && python setup.py build_ext --inplace

		# compile cython scripts
		cd .. && python setup.py build_ext --inplace


%test
	# test that the program works
	# note: not easy with this one


%environment
	# Set up environmental variables within the container
	export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
	export CFLAGS="-I/usr/local/include"
	export LDFLAGS="-L/usr/local/lib"


%runscript
	# This will be executed when the container is run (singularity run [container])
	python /fastStructure/"$@"


%help
	# This message is displayed when called as: singularity run-help [container]

	******************************************************************************

	This container is for running fastStructure

	To run, use: singularity run fastStructure.sif [args]
	So, in this case, to run a script (e.g. structure.py), use: singularity run fastStructure.sif structure.py [other args]

	Scripts available: structure.py, chooseK.py
	NOTE: distruct.py doesn't work as it depends on matplotlib and that was too complicated to set up with old python dependencies

	Check contents by entering it as: (sudo) singularity shell [container]

	******************************************************************************