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

Bioinformatics, vol. 41

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.

Authors 11

1. Pekka Ristola
   Affiliation as printed

   BioArchLinux Member , Helsinki, 00100,

   BioArchLinux member, Helsinki, Finland

2. Han Su
   Affiliation as printed

   BioArchLinux Member , Beijing, 100000,

   BioArchLinux member, Beijing, China

3. Bipin Kumar
   Affiliation as printed

   Obront Biotech Pvt. Ltd. , Hyderabad, 500007,

   Obront Biotech Pvt. Ltd, Hyderabad, India

4. Boyu Zhang

   Beijing Forestry University

   Affiliation as printed

   Beijing Forestry University , Beijing, 100083,

   Beijing Forestry University, Beijing, China

5. Yujin Hu

   Shenzhen Research Institute of Big Data

   Affiliation as printed

   Shenzhen Research Institute of Big Data , Shenzhen, 518172,

   Shenzhen Research Institute of Big Data, Shenzhen, China

6. Michael G. Elliot

   University of Groningen

   Affiliation as printed

   Department of Evolution, University of Groningen , Groningen, 9700 AB,

   Department of Evolution, University of Groningen, Groningen, Netherlands

7. Viktor Drobot

   Innate Pharma (France)

   Affiliation as printed

   Pharm InnTech LLC , Moscow, 127299, Russia

   Pharm InnTech LLC , Moscow, Russia

8. Jens Staal

   Ghent University

   Affiliation as printed

   Department of Biomedical Molecular Biology, Ghent University , 9000,

   Department of Biomedical Molecular Biology, Ghent University, Belgium

9. Martin F. Larralde Aachen

   Leiden University · Leiden University Medical Center · European Molecular Biology Laboratory

   Affiliation as printed

   Leiden University Center for Infectious Diseases, Leiden University Medical Center (LUMC) , Leiden, 2300 RA,

   Structural and Computational Biology Unit, EMBL , Heidelberg, 69117,

   Leiden University Center for Infectious Diseases, Leiden University Medical Center (LUMC), Leiden, Netherlands

   Structural and Computational Biology Unit, EMBL Heidelberg, Germany

10. Shun Wang
    Affiliation as printed

    JASP Team Member , Shenzhen, 518000,

    JASP team member , China Shenzhen

11. Haoran Yu

    Xi’an University

    Affiliation as printed

    Xi’an University , Xi’an, 710065,

    Xi'an University, Xi'an, China