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/