The Dominance Tree in Visualizing Software Dependencies

Abstract Motivation A challenge for computational biologists is to make our analyses reproducible—i.e. to rerun, combine, and share, with the assurance that equivalent runs will generate identical results. Current best practice aims at this using a combination of package managers, workflow engines, and containers. Results We present BioNix, a lightweight library built on the Nix deployment system. BioNix manages software dependencies, computational environments, and workflow stages together using a single abstraction: pure functions. This lets users specify workflows in a clean, uniform way, with strong reproducibility guarantees. Availability and Implementation BioNix is implemented in the Nix expression language and is released on GitHub under the 3-clause BSD license: https://github.com/PapenfussLab/bionix (biotools:BioNix) (BioNix, RRID:SCR_017662).

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Bringing your tools to CyVerse Discovery Environment using Docker

F1000Research ◽

10.12688/f1000research.8935.3 ◽

2016 ◽

Vol 5 ◽

pp. 1442 ◽

Cited By ~ 10

Author(s):

Upendra Kumar Devisetty ◽

Kathleen Kennedy ◽

Paul Sarando ◽

Nirav Merchant ◽

Eric Lyons

Keyword(s):

Software Tools ◽

Time Process ◽

Production Environment ◽

Scientific Software ◽

Relative Ease ◽

Ideal Candidate ◽

Software Distribution ◽

Software Dependencies ◽

The Way

Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and deployed. Docker makes the complex and time-consuming installation procedures needed for scientific software a one-time process. Because it enables platform-independent installation, versioning of software environments, and easy redeployment and reproducibility, Docker is an ideal candidate for the deployment of identical software stacks on different compute environments such as XSEDE and Amazon AWS. Cyverse's Discovery Environment also uses Docker for integrating its powerful, community-recommended software tools into CyVerse's production environment for public use. This paper will help users bring their tools into CyVerse DE which will not only allows users to integrate their tools with relative ease compared to the earlier method of tool deployment in DE but also help users to share their apps with collaborators and also release them for public use.

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