Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

Bray, S.; Bernt, M.; Soranzo, N.; van den Beek, M.; Batut, B.; Rasche, H.; Cech, M.; Cock, P.; Nekrutenko, A.; Gruning, B.; Chilton, J.

doi:10.1101/2022.03.13.483965

bioRxiv · 10.1101/2022.03.13.483965

Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

Bray, S.·Bernt, M.·Soranzo, N.·van den Beek, M.·Batut, B.·Rasche, H.·Cech, M.·Cock, P.·Nekrutenko, A.·Gruning, B.·Chilton, J.

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Abstract

There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For over a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. In order to streamline the process of integrating tools and constructing workflows as much as possible, we have developed Planemo, a software development kit for tool and workflow developers and Galaxy power users. Here we outline Planemos implementation and describe its broad range of functionality for designing, testing and executing Galaxy tools, workflows and training material. In addition, we discuss the philosophy underlying Galaxy tool and workflow development, and how Planemo encourages the use of development best practices, such as test-driven development, by its users, including those who are not professional software developers. Planemo is a mature project widely used within the Galaxy community which has been downloaded over 80,000 times.

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Bray, S., Bernt, M., Soranzo, N., van den Beek, M., Batut, B., Rasche, H., Cech, M., Cock, P., Nekrutenko, A., Gruning, B., Chilton, J.. 2022-03-14. Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses. https://doi.org/10.1101/2022.03.13.483965

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