BioArchLinux: Community-driven fresh reproducible software repository for life sciences

Guoyi Zhang; Pekka Ristola; Han Su; Bipin Kumar; Boyu Zhang; Yujin Hu; Michael G. Elliot; Viktor Drobot; Jie Zhu; Jens Staal; Martin Larralde; Shun Wang; Yun Yi; Haoran Yu

doi:10.1093/bioinformatics/btaf106

BioArchLinux: Community-driven fresh reproducible software repository for life sciences

Guoyi Zhang^*, Pekka Ristola, Han Su, Bipin Kumar, Boyu Zhang, Yujin Hu, Michael G. Elliot, Viktor Drobot, Jie Zhu, Jens Staal, Martin Larralde, Shun Wang, Yun Yi, Haoran Yu

^*Corresponding author voor dit werk

Onderzoeksoutput: Article › Academic › peer review

2 Citaten (Scopus)

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Motivation: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research. Results: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment. Availability and implementation: The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.

Originele taal-2	English
Artikelnummer	btaf106
Aantal pagina's	4
Tijdschrift	Bioinformatics
Volume	41
Nummer van het tijdschrift	3
DOI's	https://doi.org/10.1093/bioinformatics/btaf106
Status	Published - mrt.-2025

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10.1093/bioinformatics/btaf106Licentie: CC BY

BioArchLinux: community-driven fresh reproducible software repository for life sciencesFinal publisher's version, 1,09 MBLicentie: CC BY

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abstract = "Motivation: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research. Results: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment. Availability and implementation: The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.",

author = "Guoyi Zhang and Pekka Ristola and Han Su and Bipin Kumar and Boyu Zhang and Yujin Hu and Elliot, {Michael G.} and Viktor Drobot and Jie Zhu and Jens Staal and Martin Larralde and Shun Wang and Yun Yi and Haoran Yu",

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doi = "10.1093/bioinformatics/btaf106",

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AU - Zhang, Guoyi

AU - Ristola, Pekka

AU - Su, Han

AU - Kumar, Bipin

AU - Zhang, Boyu

AU - Hu, Yujin

AU - Elliot, Michael G.

AU - Drobot, Viktor

AU - Zhu, Jie

AU - Staal, Jens

AU - Larralde, Martin

AU - Wang, Shun

AU - Yi, Yun

AU - Yu, Haoran

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N2 - Motivation: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research. Results: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment. Availability and implementation: The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.

AB - Motivation: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research. Results: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment. Availability and implementation: The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.

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BioArchLinux: Community-driven fresh reproducible software repository for life sciences

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