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Containeriza*on	of	scien*fic	applica*ons	has	done	a	lot	to	make	
so6ware	more	portable	and	reproducible.	Unfortunately,	most	
high	performance	compu*ng	(HPC)	clusters	have	been	le6	out	
of	this	movement	because	of	kernel	requirements	and	security	
policy.	 In	 collabora*on	 with	 Björn	 Grüning	 represen*ng	
BioContainers	and	Vanessa	Sochat	from	the	Singularity	project,	
we	are	bringing	thousands	of	science	apps	to	any	cluster	that	
can	run	Singularity.	
BioContainers	for	supercomputers:	
2,000+	accessible,	discoverable	Singularity	apps		
John	M.	Fonner,	Rion	Dooley,		
Jacquelyn	Turcinovic,	MaWhew	W.	Vaughn	
Introduc)on	
Singularity	Hub	
singularity-hub.org	
BioConda	
bioconda.github.io	
BioContainers	
biocontainers.pro	
Key	Capabili)es	
•  All	 TACC	 HPC	 systems	 now	 support	
Singularity	images	and	BioContainers	
•  Cyverse	 supports	 BioContainers	 via	
Docker	 on	 their	 cloud	 resources	 and	
now	via	Singularity	on	HPC	resources	
•  Convert	 your	 own	 Docker	 containers	
to	 Singularity	 for	 use	 at	 TACC	 using	
github.com/TACC/docker2singularity	
Future	Work	
•  Con*nuous	integra*on	from	BioConda	
to	TACC	/	Singularity	Hub	
•  Enroll	 as	 a	 Singularity	 Registry	 on	
Singularity	Hub	
•  Explore	 GPUs/co-processors	 support	
and	custom	writable	directories	
•  On-demand	 conversion	 of	 Docker	
containers	to	Singularity		
BioConda	has	over	2,400	recipes	for	bioinforma*cs	apps	thanks	
to	the	contribu*ons	of	many	researchers	and	developers.	The	
Cyverse	 project	 has	 adopted	 Conda	 recipes	 as	 the	 primary	
method	for	integra*ng	new	apps	into	their	infrastructure.	
BioContainers	has	automated	the	process	of	conver*ng	Conda	
recipes	into	so6ware	containers	and	has	woven	their	framework	
directly	 into	 BioConda.	 All	 Docker	 containers	 are	 con*nuously	
registered	with	a	Quay.io	repository.	
Singularity-Hub	 supports	 integra*on	 with	 GitHub	 to	 generate	
Singularity	 images	 based	 on	 git	 commits.	 They	 are	 extending	
their	code-base	to	support	ins*tu*onal	repositories	of	images.	
TACC	 has	 installed	 Singularity	 run*me	 support	 on	 its	 HPC	
systems,	 has	 converted	 all	 BioContainer	 apps	 to	 Singularity	
images,	 and	 has	 made	 them	 available	 to	 XSEDE,	 TACC,	 and	
Cyverse	 users.	 Public,	 unauthen*cated	 download	 will	 be	
available	as	soon	as	possible	through	Singularity	Hub.	
Summary	
Get	involved	
•  Contribute	your	bioinforma*cs	apps	to	
BioConda	and	join	the	community	
•  Try	 out	 Singularity	 at	 TACC	 through	
either	xsede.org	or	tacc.utexas.edu	
•  Chime	in	on	our	development	effort:	
github.com/TACC/docker2singularity	
singularityhub.github.io/singularity-
registry/

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BioContainers for supercomputers: 2,000+ accessible, discoverable Singularity apps

  • 1. Containeriza*on of scien*fic applica*ons has done a lot to make so6ware more portable and reproducible. Unfortunately, most high performance compu*ng (HPC) clusters have been le6 out of this movement because of kernel requirements and security policy. In collabora*on with Björn Grüning represen*ng BioContainers and Vanessa Sochat from the Singularity project, we are bringing thousands of science apps to any cluster that can run Singularity. BioContainers for supercomputers: 2,000+ accessible, discoverable Singularity apps John M. Fonner, Rion Dooley, Jacquelyn Turcinovic, MaWhew W. Vaughn Introduc)on Singularity Hub singularity-hub.org BioConda bioconda.github.io BioContainers biocontainers.pro Key Capabili)es •  All TACC HPC systems now support Singularity images and BioContainers •  Cyverse supports BioContainers via Docker on their cloud resources and now via Singularity on HPC resources •  Convert your own Docker containers to Singularity for use at TACC using github.com/TACC/docker2singularity Future Work •  Con*nuous integra*on from BioConda to TACC / Singularity Hub •  Enroll as a Singularity Registry on Singularity Hub •  Explore GPUs/co-processors support and custom writable directories •  On-demand conversion of Docker containers to Singularity BioConda has over 2,400 recipes for bioinforma*cs apps thanks to the contribu*ons of many researchers and developers. The Cyverse project has adopted Conda recipes as the primary method for integra*ng new apps into their infrastructure. BioContainers has automated the process of conver*ng Conda recipes into so6ware containers and has woven their framework directly into BioConda. All Docker containers are con*nuously registered with a Quay.io repository. Singularity-Hub supports integra*on with GitHub to generate Singularity images based on git commits. They are extending their code-base to support ins*tu*onal repositories of images. TACC has installed Singularity run*me support on its HPC systems, has converted all BioContainer apps to Singularity images, and has made them available to XSEDE, TACC, and Cyverse users. Public, unauthen*cated download will be available as soon as possible through Singularity Hub. Summary Get involved •  Contribute your bioinforma*cs apps to BioConda and join the community •  Try out Singularity at TACC through either xsede.org or tacc.utexas.edu •  Chime in on our development effort: github.com/TACC/docker2singularity singularityhub.github.io/singularity- registry/