shubavarshini/microbiome:def

$ singularity pull shub://shubavarshini/microbiome:def

Singularity Recipe

Bootstrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
Stage: building

%files

%environment

%runscript
	echo "testing installations"

%post
	apt-get -y install software-properties-common
	apt-get -y update
	add-apt-repository main
	add-apt-repository universe
	add-apt-repository restricted
	add-apt-repository multiverse
	apt-get -y update
	apt-get -y install git wget python python3 python-pip python3-pip
	
	apt-get -y install gcc make zlib1g-dev libbz2-dev libncurses5-dev libncursesw5-dev liblzma-dev

	pip install --upgrade setuptools --user python
	#pip3 install --upgrade setuptools --user python3
	
	apt-get -y install mash centrifuge mummer prodigal
	
	wget https://ani.jgi.doe.gov/download_files/ANIcalculator_v1.tgz
	tar zxvf ANIcalculator_v1.tgz
	#path=`pwd`
	#echo "export PATH=\"/ANIcalculator_v1/:$PATH\"" >>$SINGULARITY_ENVIRONMENT
	pip install numpy
	pip install pysam
	pip install checkm-genome
	#wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
	#tar xvzf checkm_data_2015_01_16.tar.gz
	#checkm data setRoot .
	pip3 install drep
	#echo "export PATH=\"/usr/local/bin/:$PATH\"" >>$SINGULARITY_ENVIRONMENT
	

%labels
	Author sva
	Type testing

%help
	This is a testing container for drep and checkm.

Stage: installingSoftwares

%post
	#python2.7 -m pip install numpy
	#python2.7 -m pip install pysam
	#python2.7 -m pip install checkm-genome
	#python3.6 -m pip install drep
	

%test
	#dRep bonus testDir --check_dependencies

Collection

• Name: shubavarshini/microbiome
• License: None

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