Container

Developed for last years tutorial using a singularity definition file. As you can see using a conda yaml file with Docker is much cleaner.
Bootstrap: debootstrap
OSversion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/

%labels
	RNA-Seq tutorial
	Installs: Samtools, Hisat2, Kallisto, Stringtie and gffcompare
	This image contains all the tools to perform reference
	guided and reference free RNA Seq analysis.

%environment
	export LC_ALL=C.UTF-8
	export LANG=C.UTF-8
	PATH="/usr/bin/:$PATH"

%post
	apt-get update
        apt-get -y install \
                build-essential \
                wget \
                tar \
                unzip \
                sudo \
                vim \
                software-properties-common

	sudo add-apt-repository universe
        sudo add-apt-repository restricted
        sudo add-apt-repository multiverse

	sudo apt-get -y install \
		samtools

	mkdir -p repo/
	cd repo/
	wget --no-check-certificate http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.11.5.Linux_x86_64.tar.gz
	tar -xvzf gffcompare-0.11.5.Linux_x86_64.tar.gz
	sudo chmod 777 /repo/gffcompare-0.11.5.Linux_x86_64/gffcompare
	sudo ln -s /repo/gffcompare-0.11.5.Linux_x86_64/gffcompare /usr/bin/gffcompare
	rm gffcompare-0.11.5.Linux_x86_64.tar.gz

	wget --no-check-certificate http://ccb.jhu.edu/software/stringtie/dl/stringtie-2.0.6.Linux_x86_64.tar.gz
	tar -xvzf stringtie-2.0.6.Linux_x86_64.tar.gz
	sudo chmod 777 /repo/stringtie-2.0.6.Linux_x86_64/stringtie
	sudo ln -s /repo/stringtie-2.0.6.Linux_x86_64/stringtie /usr/bin/stringtie
	rm stringtie-2.0.6.Linux_x86_64.tar.gz

	wget --no-check-certificate ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-Linux_x86_64.zip
	unzip hisat2-2.1.0-Linux_x86_64.zip
	sudo chmod 777 /repo/hisat2-2.1.0/hisat2*
	sudo cp /repo/hisat2-2.1.0/hisat2* /usr/bin/
	rm hisat2-2.1.0-Linux_x86_64.zip

	wget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.46.1/kallisto_linux-v0.46.1.tar.gz
	tar -xvzf kallisto_linux-v0.46.1.tar.gz
	sudo chmod 777 /repo/kallisto/kallisto
	sudo cp /repo/kallisto/kallisto /usr/bin/
	rm kallisto_linux-v0.46.1.tar.gz
Genomic Data Analysis II

Container
