Conda, Container and Bots
How to Build and Maintain Tool Dependencies in Workflows and Training Materials
DOI:
https://doi.org/10.52825/cordi.v1i.417Keywords:
conda, containers, bots, automation, GalaxyAbstract
Abstract. The lifecycle of scientific tools comprises the creation of code releases, packages and containers which can be deployed into cloud platforms, such as the Galaxy Project, where they are run and integrated into workflows. The tools and workflows are further used to create training material that benefits a broad community. The need to organize and streamline this tool development lifecycle has led to a sophisticated development and deployment architecture.
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References
“Galaxy Europe.” https://usegalaxy.eu (accessed Apr. 24, 2023).
“Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update | Nucleic Acids Research | Oxford Academic.” doi: 10.1093/nar/gkac247 DOI: https://doi.org/10.1093/nar/gkac247
“Conda — conda documentation.” https://docs.conda.io/en/latest/ (accessed Apr. 26, 2023).
J. Janssen et al., “pyiron: An integrated development environment for computational materials science,” Computational Materials Science, vol. 163, pp. 24–36, Jun. 2019, doi: 10.1016/j.commatsci.2018.07.043. DOI: https://doi.org/10.1016/j.commatsci.2018.07.043
B. Grüning et al., “Bioconda: sustainable and comprehensive software distribution for the life sciences,” Nat Methods, vol. 15, no. 7, Art. no. 7, Jul. 2018, doi: 10.1038/s41592-018-0046-7. DOI: https://doi.org/10.1038/s41592-018-0046-7
F. da Veiga Leprevost et al., “BioContainers: an open-source and community-driven framework for software standardization,” Bioinformatics, vol. 33, no. 16, pp. 2580–2582, Aug. 2017, doi: 10.1093/bioinformatics/btx192. DOI: https://doi.org/10.1093/bioinformatics/btx192
“Quay Container Registry · Quay.” https://quay.io/organization/biocontainers (accessed Apr. 26, 2023).
“Index of /singularity/.” https://depot.galaxyproject.org/singularity/ (accessed Apr. 26, 2023).
S. Bray et al., “The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond,” Genome Res, vol. 33, no. 2, pp. 261–268, Feb. 2023, doi: 10.1101/gr.276963.122. DOI: https://doi.org/10.1101/gr.276963.122
“Galaxy Training,” Galaxy Training Network. https://training.galaxyproject.org/training-material/ (accessed Apr. 26, 2023).
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Copyright (c) 2023 Paul Zierep, Sanjay Kumar Srikakulam , Sebastian Schaaf, Bjoern Gruening
This work is licensed under a Creative Commons Attribution 4.0 International License.
Accepted 2023-06-30
Published 2023-09-07
