Recommendations for the packaging and containerizing of bioinformatics software

Bjorn Gruening (1) , Olivier Sallou (2) , Pablo Moreno (3) , Felipe da Veiga Leprevost (4) , Hervé Ménager (5) , Dan Søndergaard (6) , Hannes Röst (7) , Timo Sachsenberg (8) , Brian O'Connor (9) , Fábio Madeira (3) , Victoria Dominguez del Angel (10, 11) , Michael Crusoe (12) , Susheel Varma (3) , Daniel Blankenberg (13) , Rafael Jimenez (14) , Yasset Perez-Riverol (3) , Biocontainers Community

1 Department of Computer Science [Freiburg]
2 IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires
3 EMBL-EBI - European Bioinformatics Institute [Hinxton]
4 Department of Pathology [Ann Arbor, USA]
5 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
6 Bioinformatics Research Centre
7 Donnelly Centre [Toronto, ON, Canada]
8 Wilhelm-Schickard-Institut für Informatik [Tübingen]
9 Santa Cruz Genomics Institute
10 Université Paris-Saclay
11 IFB-CORE - Institut Français de Bioinformatique - UMS CNRS 3601
12 Department of Microbiology and Molecular Genetics
13 Genomic Medicine Institute [Cleveland]
14 ELIXIR Hub [Cambridge]

Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent. They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software.

Keywords: containers and packages; best practices bioinformatics; reproducibility

Domains: Computer Science [cs]; Bioinformatics [q-bio.QM]

Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, et al.. Recommendations for the packaging and containerizing of bioinformatics software. F1000Research, 2018, 7, pp.742. ⟨10.12688/f1000research.15140.2⟩. ⟨pasteur-02769991⟩