Boutiques: a flexible framework to integrate command-line applications in computing platforms

Tristan Glatard; Gregory Kiar; Tristan Aumentado-Armstrong; Natacha Beck; Pierre Bellec; Rémi Bernard; Axel Bonnet; Shawn T. Brown; Sorina Camarasu-Pop; Frédéric Cervenansky; Samir Das; Rafael Ferreira da Silva; Guillaume Flandin; Pascal Girard; Krzysztof J. Gorgolewski; Charles R.G. Guttmann; Valérie Hayot-Sasson; Pierre Olivier Quirion; Pierre Rioux; Marc Étienne Rousseau; Alan C. Evans

doi:10.1093/gigascience/giy016

Boutiques: a flexible framework to integrate command-line applications in computing platforms

Tristan Glatard, Gregory Kiar, Tristan Aumentado-Armstrong, Natacha Beck, Pierre Bellec, Rémi Bernard, Axel Bonnet, Shawn T. Brown, Sorina Camarasu-Pop, Frédéric Cervenansky, Samir Das, Rafael Ferreira da Silva, Guillaume Flandin, Pascal Girard, Krzysztof J. Gorgolewski, Charles R.G. Guttmann, Valérie Hayot-Sasson, Pierre Olivier Quirion, Pierre Rioux, Marc Étienne RousseauAlan C. Evans

Research output: Contribution to journal › Article › peer-review

25 Scopus citations

Abstract

We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.

Original language	English
Journal	GigaScience
Volume	7
Issue number	5
DOIs	https://doi.org/10.1093/gigascience/giy016
State	Published - May 1 2018
Externally published	Yes

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Glatard, T., Kiar, G., Aumentado-Armstrong, T., Beck, N., Bellec, P., Bernard, R., Bonnet, A., Brown, S. T., Camarasu-Pop, S., Cervenansky, F., Das, S., Ferreira da Silva, R., Flandin, G., Girard, P., Gorgolewski, K. J., Guttmann, C. R. G., Hayot-Sasson, V., Quirion, P. O., Rioux, P., ... Evans, A. C. (2018). Boutiques: a flexible framework to integrate command-line applications in computing platforms. GigaScience, 7(5). https://doi.org/10.1093/gigascience/giy016

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title = "Boutiques: a flexible framework to integrate command-line applications in computing platforms",

abstract = "We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.",

author = "Tristan Glatard and Gregory Kiar and Tristan Aumentado-Armstrong and Natacha Beck and Pierre Bellec and R{\'e}mi Bernard and Axel Bonnet and Brown, {Shawn T.} and Sorina Camarasu-Pop and Fr{\'e}d{\'e}ric Cervenansky and Samir Das and {Ferreira da Silva}, Rafael and Guillaume Flandin and Pascal Girard and Gorgolewski, {Krzysztof J.} and Guttmann, {Charles R.G.} and Val{\'e}rie Hayot-Sasson and Quirion, {Pierre Olivier} and Pierre Rioux and Rousseau, {Marc {\'E}tienne} and Evans, {Alan C.}",

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doi = "10.1093/gigascience/giy016",

language = "English",

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Glatard, T, Kiar, G, Aumentado-Armstrong, T, Beck, N, Bellec, P, Bernard, R, Bonnet, A, Brown, ST, Camarasu-Pop, S, Cervenansky, F, Das, S, Ferreira da Silva, R, Flandin, G, Girard, P, Gorgolewski, KJ, Guttmann, CRG, Hayot-Sasson, V, Quirion, PO, Rioux, P, Rousseau, MÉ & Evans, AC 2018, 'Boutiques: a flexible framework to integrate command-line applications in computing platforms', GigaScience, vol. 7, no. 5. https://doi.org/10.1093/gigascience/giy016

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T2 - a flexible framework to integrate command-line applications in computing platforms

AU - Glatard, Tristan

AU - Kiar, Gregory

AU - Aumentado-Armstrong, Tristan

AU - Beck, Natacha

AU - Bellec, Pierre

AU - Bernard, Rémi

AU - Bonnet, Axel

AU - Brown, Shawn T.

AU - Camarasu-Pop, Sorina

AU - Cervenansky, Frédéric

AU - Das, Samir

AU - Ferreira da Silva, Rafael

AU - Flandin, Guillaume

AU - Girard, Pascal

AU - Gorgolewski, Krzysztof J.

AU - Guttmann, Charles R.G.

AU - Hayot-Sasson, Valérie

AU - Quirion, Pierre Olivier

AU - Rioux, Pierre

AU - Rousseau, Marc Étienne

AU - Evans, Alan C.

PY - 2018/5/1

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AB - We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.

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JO - GigaScience

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Boutiques: a flexible framework to integrate command-line applications in computing platforms

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