The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

Simon Bray; John Chilton; Matthias Bernt; Nicola Soranzo; Marius van den Beek; Bérénice Batut; Helena Rasche; Martin Čech; Peter J.A. Cock; Björn Grüning; Anton Nekrutenko

doi:10.1101/gr.276963.122

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek, Bérénice Batut, Helena Rasche, Martin Čech, Peter J.A. Cock, Björn Grüning, Anton Nekrutenko^*

^*Corresponding author for this work

Pathology

Research output: Contribution to journal › Article › Academic › peer-review

1 Citation (Scopus)

Abstract

There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than 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. 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 Planemo’s 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.

Original language	English
Pages (from-to)	261-268
Number of pages	8
Journal	Genome Research
Volume	33
Issue number	3
DOIs	https://doi.org/10.1101/gr.276963.122
Publication status	Published - Mar 2023

Bibliographical note

Acknowledgments:
We thank the broader Galaxy community for their support and software development efforts. This work is funded by National Institutes of Health grant U41 HG006620 and National Science Foundation ABI grant 1661497. Usegalaxy.eu is supported by the German Federal Ministry of Education and Research grants 031L0101C and de.NBI-epi to B.G. Usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons through funding from the Australian Government National Collaborative Research Infrastructure Strategy. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright: © 2023 Bray et al.

Access to Document

10.1101/gr.276963.122Licence: CC BY

Genome Res.-2023-Bray-261-8Final published version, 2.1 MBLicence: CC BY

Cite this

@article{19832cec4c6741a1900562cc01fcedda,

title = "The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond",

abstract = "There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than 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. 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 Planemo{\textquoteright}s 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.",

author = "Simon Bray and John Chilton and Matthias Bernt and Nicola Soranzo and {van den Beek}, Marius and B{\'e}r{\'e}nice Batut and Helena Rasche and Martin {\v C}ech and Cock, {Peter J.A.} and Bj{\"o}rn Gr{\"u}ning and Anton Nekrutenko",

note = "Acknowledgments: We thank the broader Galaxy community for their support and software development efforts. This work is funded by National Institutes of Health grant U41 HG006620 and National Science Foundation ABI grant 1661497. Usegalaxy.eu is supported by the German Federal Ministry of Education and Research grants 031L0101C and de.NBI-epi to B.G. Usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons through funding from the Australian Government National Collaborative Research Infrastructure Strategy. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: {\textcopyright} 2023 Bray et al.",

year = "2023",

month = mar,

doi = "10.1101/gr.276963.122",

language = "English",

volume = "33",

pages = "261--268",

journal = "Genome Research",

issn = "1088-9051",

publisher = "Cold Spring Harbor Laboratory Press",

number = "3",

}

TY - JOUR

T1 - The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

AU - Bray, Simon

AU - Chilton, John

AU - Bernt, Matthias

AU - Soranzo, Nicola

AU - van den Beek, Marius

AU - Batut, Bérénice

AU - Rasche, Helena

AU - Čech, Martin

AU - Cock, Peter J.A.

AU - Grüning, Björn

AU - Nekrutenko, Anton

N1 - Acknowledgments: We thank the broader Galaxy community for their support and software development efforts. This work is funded by National Institutes of Health grant U41 HG006620 and National Science Foundation ABI grant 1661497. Usegalaxy.eu is supported by the German Federal Ministry of Education and Research grants 031L0101C and de.NBI-epi to B.G. Usegalaxy.org.au is supported by Bioplatforms Australia and the Australian Research Data Commons through funding from the Australian Government National Collaborative Research Infrastructure Strategy. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2023 Bray et al.

PY - 2023/3

Y1 - 2023/3

N2 - There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than 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. 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 Planemo’s 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.

AB - There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than 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. 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 Planemo’s 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.

UR - http://www.scopus.com/inward/record.url?scp=85149999450&partnerID=8YFLogxK

U2 - 10.1101/gr.276963.122

DO - 10.1101/gr.276963.122

M3 - Article

C2 - 36828587

AN - SCOPUS:85149999450

SN - 1088-9051

VL - 33

SP - 261

EP - 268

JO - Genome Research

JF - Genome Research

IS - 3

ER -

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this