ous-uio-bioinfo-core/containerised_ATACseq_pipeline:atacseqqc

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

Singularity Recipe

Bootstrap: docker
From: ubuntu:bionic-20191029

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

%post
	apt-get update && apt-get install -y wget
	wget https://repo.anaconda.com/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"
	export PATH=${CONDA}:${PATH}

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

	conda install -y \
		bioconductor-atacseqqc=1.12.0 \
		bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.3 \
		bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.10.0 \
		bioconductor-phastcons100way.ucsc.hg38=3.7.1 \
		bioconductor-bsgenome.hsapiens.ucsc.hg19=1.4.3 \
		bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2 \
		bioconductor-phastcons100way.ucsc.hg19=3.7.2 \
		bioconductor-chippeakanno=3.22.0 \
		bioconductor-genomicalignments=1.24.0 \
		bioconductor-motifdb=1.30.0 \
		r-runit \
		bioconductor-seqlogo \
		bioconductor-biocstyle \
		r-knitr \
		r-markdown \
		r-futile.logger \
		xorg-libxt \
		fonts-conda-ecosystem=1
            
	echo "PATH=${PATH}"            

	mkdir /cluster /work /tsd /projects

%runscript
	echo "Running ubuntu bionic container with ATACseqQC v1.12.0"
	exec /bin/bash "$@"

Collection

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

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