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

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 ra...

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Autores principales: Bray, Simon, Chilton, John, Bernt, Matthias, Soranzo, Nicola, van den Beek, Marius, Batut, Bérénice, Rasche, Helena, Čech, Martin, Cock, Peter J.A., Grüning, Björn, Nekrutenko, Anton
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10069471/
https://www.ncbi.nlm.nih.gov/pubmed/36828587
http://dx.doi.org/10.1101/gr.276963.122
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author Bray, Simon
Chilton, John
Bernt, Matthias
Soranzo, Nicola
van den Beek, Marius
Batut, Bérénice
Rasche, Helena
Čech, Martin
Cock, Peter J.A.
Grüning, Björn
Nekrutenko, Anton
author_facet Bray, Simon
Chilton, John
Bernt, Matthias
Soranzo, Nicola
van den Beek, Marius
Batut, Bérénice
Rasche, Helena
Čech, Martin
Cock, Peter J.A.
Grüning, Björn
Nekrutenko, Anton
author_sort Bray, Simon
collection PubMed
description 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.
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spelling pubmed-100694712023-04-04 The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond Bray, Simon Chilton, John Bernt, Matthias Soranzo, Nicola van den Beek, Marius Batut, Bérénice Rasche, Helena Čech, Martin Cock, Peter J.A. Grüning, Björn Nekrutenko, Anton Genome Res Resources 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. Cold Spring Harbor Laboratory Press 2023-02 /pmc/articles/PMC10069471/ /pubmed/36828587 http://dx.doi.org/10.1101/gr.276963.122 Text en © 2023 Bray et al.; Published by Cold Spring Harbor Laboratory Press https://creativecommons.org/licenses/by/4.0/This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Resources
Bray, Simon
Chilton, John
Bernt, Matthias
Soranzo, Nicola
van den Beek, Marius
Batut, Bérénice
Rasche, Helena
Čech, Martin
Cock, Peter J.A.
Grüning, Björn
Nekrutenko, Anton
The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
title The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
title_full The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
title_fullStr The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
title_full_unstemmed The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
title_short The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
title_sort planemo toolkit for developing, deploying, and executing scientific data analyses in galaxy and beyond
topic Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10069471/
https://www.ncbi.nlm.nih.gov/pubmed/36828587
http://dx.doi.org/10.1101/gr.276963.122
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