ScreenProcessing.def

Bootstrap: docker
From: ubuntu:20.04

%post
	apt update
	apt upgrade -y

	###set local time
	apt install -y tzdata
	ln -sf /usr/share/zoneinfo/US/Pacific /etc/localtime

	### common prerequisites
	apt install -y git python3 python3-pip

	# Screen Processing from mhorlbeck repo; credit to Scot Federman for adding Singularity installation option
	# Consider also UCSF LGR repo if there are more up-to-date commits
	git clone https://github.com/mhorlbeck/ScreenProcessing.git

	# This is derived from the GitHub repo above
	pip install -r ScreenProcessing/requirements.txt

	# clean up
	apt autoremove
%labels
	Author "Scot Federman"
	Version v1.0
%help
	This is a container used to run Screen Processing, a bioinformatics pipeline to analyze sequencing data from pooled screens.
%environment
	export PATH=$PATH:/ScreenProcessing