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

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

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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.

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

  1. 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/

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