QuaCK_singularity_recipe_file.txt

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

%help
	This container is built to run the QuaCK repo located on github: https://github.com/tbrunetti/QuaCK

%setup
	cp run_GWAS_QC_filtering_pipeline.py $SINGULARITY_ROOTFS
	cp run_GWAS_QC_filtering_pipeline.py.json $SINGULARITY_ROOTFS
	cp run_GWAS_QC_filtering_pipeline.json $SINGULARITY_ROOTFS
	echo $SINGULARITY_ROOTFS
	ls $SINGULARITY_ROOTFS

%files
	LICENSE
	format_sample_sheet_names.py /mnt
	generate_illumina_snp_stats.py /mnt
	generate_report.py /mnt
	hapmap_trio_info.txt /mnt
	Parameter_Definitions.pdf /mnt
	pre-QC-initialization-workflow.pdf /mnt
	pre-QC-initialization-workflow.png /mnt
	QC-pipeline-workflow.pdf /mnt
	QC-pipeline-workflow.png /mnt
	run_GWAS_QC_filtering_pipeline.py /mnt
	transparent_AMC_cropped.png /mnt
	new_TGP_vol1_MEGA_flipped_triallelic_removed_no_atgc.bed /mnt
	new_TGP_vol1_MEGA_flipped_triallelic_removed_no_atgc.bim /mnt
	new_TGP_vol1_MEGA_flipped_triallelic_removed_no_atgc.fam /mnt
	run_GWAS_QC_filtering_pipeline.py.json /mnt
	run_GWAS_QC_filtering_pipeline.json /mnt
	plink /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==2.2.4
	pip install fpdf
	pip install Pillow
	pip install pypdf2
	pip install statistics
	pip install xlrd
	pip install scipy==1.2.0
	pip install seaborn==0.8.0
	/usr/local/bin/chunky init /mnt
	cp run_GWAS_QC_filtering_pipeline.py /mnt/.chunky/pipelines
	cp run_GWAS_QC_filtering_pipeline.py.json /mnt/.chunky/configs
	cp run_GWAS_QC_filtering_pipeline.py /mnt/.chunky/pipelines/run_GWAS_QC_filtering_pipeline
	cp run_GWAS_QC_filtering_pipeline.json /mnt/.chunky/configs
	cd /mnt
	ls
	chmod -R a+rwx /mnt
	chmod -R a+rwx /mnt/.chunky

%environment
	CHUNKY_HOME=/mnt
	export CHUNKY_HOME
	export PATH="${PATH}:/mnt:/usr/bin:/bin:/usr/local/sbin/:/usr/local/bin"
	export PYTHONPATH="${PYTHONPATH}:/mnt"
	export PYTHONPATH="${PYTHONPATH}:/usr/local/bin/:/usr/lib/python2.7/:/usr/bin/"