Container-based bioinformatics with Pachyderm.

ABSTRACT:

Motivation

Computational biologists face many challenges related to data size, and they need to manage complicated analyses often including multiple stages and multiple tools, all of which must be deployed to modern infrastructures. To address these challenges and maintain reproducibility of results, researchers need (i) a reliable way to run processing stages in any computational environment, (ii) a well-defined way to orchestrate those processing stages and (iii) a data management layer that tracks data as it moves through the processing pipeline.

Results

Pachyderm is an open-source workflow system and data management framework that fulfils these needs by creating a data pipelining and data versioning layer on top of projects from the container ecosystem, having Kubernetes

SUBMITTER: Novella JA 

PROVIDER: S-EPMC6394392 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature