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

Containerization of scientific applications has done a lot to make software more portable and reproducible. Unfortunately, most HPC clusters have been left out of this movement because of kernel requirements and security policy. In collaboration with Björn Grüning representing BioContainers and Vanessa Sochat from the Singularity project, we are bringing thousands of science apps to any cluster that can run Singularity.

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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/
Ad

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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/