ous-uio-bioinfo-core/containerised_ATACseq_pipeline:picard

$ singularity pull shub://ous-uio-bioinfo-core/containerised_ATACseq_pipeline:picard

Singularity Recipe

Bootstrap: docker
From: ubuntu:bionic-20191029

%environment
	CONDA="/usr/local/miniconda3/bin"
	PATH="${CONDA}:${PATH}"
	export PATH

%post
	apt-get update && apt-get install -y wget
	wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
	bash Miniconda3-latest-Linux-x86_64.sh -b -f -u -p /usr/local/miniconda3
	rm Miniconda3-latest-Linux-x86_64.sh

	CONDA="/usr/local/miniconda3/bin"
	PATH="${CONDA}:${PATH}"
	export PATH

	conda config --add channels conda-forge
	conda config --add channels bioconda 

	conda install -y \
		picard=2.23.3 \
		r-base=3.6.2 \
		fonts-conda-ecosystem=1

	echo "PATH=${PATH}"

	mkdir /cluster /work /tsd /projects                  
      
%runscript
	echo "Running ubuntu bionic container with picard v2.23.3 and R v3.6.2"
	exec /bin/bash "$@"

Collection

• Name: ous-uio-bioinfo-core/containerised_ATACseq_pipeline
• License: MIT License

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