Singularity.tools.def

Bootstrap: docker
From: conda/miniconda3-centos7
Include: yum which wget


%environment
	alias python=python3

%post

	yum makecache fast && yum update -y
	yum -y install git bzip2 wget which sudo vi
	yum -y group install "Development Tools"

	conda update -y conda
	conda remove -y asn1crypto
	conda install -c conda-forge -c bioconda -y asn1crypto kallisto=0.44.0 diamond=0.9.34 bedtools=2.29.2 blast=2.9.0 biopython numpy genometools-genometools=1.5.10 gffread=0.11.6 seqkit=2.1.0

	mkdir -p /opt/software
	cd /opt/software
	git clone --depth=1 https://github.com/EI-CoreBioinformatics/CPC2
	cd CPC2
	python3 setup.py bdist_wheel && pip3 install dist/*whl

	CPC2 --help

	conda clean --all --yes