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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...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2023
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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. |
format | Online Article Text |
id | pubmed-10069471 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
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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