CCPM_Biobank_Freeze_and_Clinical_Validation_Software_v0.1.0_07192020.txt

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

%help
	This container contains software for the CCPM biobank pertaining to biobank data qc, freeze generation, and gtc manipulations and validations. See documentation of packages at: https://github.com/tbrunetti/GThaCk and https://github.com/Illumina/GTCtoVCF

%setup

%post
	echo "Installing all container dependencies!"
	apt-get -y update
	apt-get install -y software-properties-common
	apt-get install -y gpgv gpgsm gnupg-l10n gnupg
	apt-get -y install git
	add-apt-repository universe
	apt-get -y install libpcre2-8-0 libcurl4-openssl-dev
	apt-get install -y build-essential zlib1g-dev libncurses5-dev  libgdbm-dev libnss3-dev libssl-dev libreadline-dev libffi-dev wget
	add-apt-repository ppa:deadsnakes/ppa
	apt-get -y update
	apt-get -y install autoconf
	apt-get -y install automake
	apt-get -y install libbz2-dev
	apt-get -y install liblzma-dev
	apt-get -y install libgsl0-dev
	apt-get -y install perl
	wget https://github.com/Kitware/CMake/releases/download/v3.15.2/cmake-3.15.2.tar.gz
	tar -zxvf cmake-3.15.2.tar.gz
	cd cmake-3.15.2
	./bootstrap
	make
	make install
	apt-get -y install libssl1.1
	apt-get -y install libxml2-dev
	apt-get -y install python3
	apt-get -y install python3-pip
	apt-get -y install python3-dev
	apt-get -y install 2to3
	apt-get -y install python3-lib2to3
	apt-get install python3-toolz
	pip3 install cget
	pip3 install numpy
	pip3 install pandas
	pip3 install matplotlib
	pip3 install seaborn
	pip3 install pysam
	pip3 install pyvcf
	pip3 install Cython
	which python3
	ln -s /usr/bin/python3 /usr/bin/python
	export LC_ALL=C.UTF-8
    	export LANG=C.UTF-8
	apt-get -y update
	cd /opt/
        git clone https://github.com/samtools/htslib.git
        cd /opt/htslib/
        autoheader
        autoconf -Wno-syntax
        ./configure
        make
        make install
	cd /opt/
	git clone https://github.com/samtools/samtools.git
	cd /opt/samtools/
	autoheader
	autoconf -Wno-syntax
	./configure 
	make
	make install
	cd /opt/
	git clone git://github.com/samtools/bcftools.git 
	cd bcftools
	autoheader && autoconf && ./configure --enable-libgsl
	make
	make install
	cd /opt/
	git clone https://github.com/tbrunetti/GThaCk.git
	cd /opt/GThaCk/modules
	mv IlluminaBeadArrayFiles.tar.gz /usr/local/lib/python3.6/dist-packages/
	cd /usr/local/lib/python3.6/dist-packages/
	tar -zxvf IlluminaBeadArrayFiles.tar.gz
	cd /opt/
	git clone https://github.com/Illumina/GTCtoVCF.git
	cd /opt/GTCtoVCF/scripts
	./download_reference.sh 37
	./download_reference.sh 38

%files

%environment
	export NETCDF_INCLUDE=/usr/include
	export PATH="${PATH}:/mnt:/opt/GTCtoVCF:/opt/:/opt/GThaCk/:/usr/bin:/bin:/usr/local/sbin/:/usr/local/bin"
        export PYTHONPATH="${PYTHONPATH}:/mnt/:/opt/"
        export PYTHONPATH="${PYTHONPATH}:/usr/local/bin/:/usr/local/lib/python3.6/dist-packages/:/usr/local/lib/python3.6/:/usr/bin/"

%runscript
	exec "$@"