GP3_singularity_recipe

Bootstrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
Include: apt

%help
	This container is built to run the GP3 repo located on github

%setup
	cp run_GWAS_analysis_pipeline.py $SINGULARITY_ROOTFS
	cp run_GWAS_analysis_pipeline.py.json $SINGULARITY_ROOTFS
	echo $SINGULARITY_ROOTFS
	ls $SINGULARITY_ROOTFS
%files
	LICENSE
	PCA_indi.R /mnt
	PCA_TGP.R /mnt
	run_GWAS_analysis_pipeline.py mnt
	GENESIS_setup_ANALYSIS_PIPELINE.R /mnt
	sample_sheet_template.xlsx /mnt
	summary_stats.py /mnt
	TGP_Sub_and_SuperPopulation_info.txt /mnt
	king /mnt
	plink /mnt
	run_GWAS_analysis_pipeline.py.json mnt

%runscript
	echo "chunkypipes framework is ready!"
	cd /mnt
	exec /usr/local/bin/chunky "$@"

%post
	echo "Installing all container dependencies!"
	apt-get -y update
	apt-get -y install software-properties-common
	apt-add-repository universe
	apt-get -y update
	apt-get -y install python
	apt-get -y install python-pip
	echo "verifiying pip install"
	pip -V
	pip install chunkypipes
	pip install pandas
	pip install numpy
	pip install matplotlib
	pip install fpdf
	pip install Pillow
	pip install pypdf2
	pip install statistics
	pip install xlrd
	apt-get -y install r-base
	/usr/local/bin/chunky init /mnt
	mv run_GWAS_analysis_pipeline.py /mnt/.chunky/pipelines
	mv run_GWAS_analysis_pipeline.py.json /mnt/.chunky/configs
	cd /mnt
	ls
	chmod a+rwx /mnt
        chmod -R a+rwx /mnt/.chunky

%environment
	CHUNKY_HOME=/mnt
	export CHUNKY_HOME
	export PYTHONPATH="${PYTHONPATH}:/mnt/"