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. 2018 May 1;7(5):giy016.
doi: 10.1093/gigascience/giy016.

Boutiques: A Flexible Framework to Integrate Command-Line Applications in Computing Platforms

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Free PMC article

Boutiques: A Flexible Framework to Integrate Command-Line Applications in Computing Platforms

Tristan Glatard et al. Gigascience. .
Free PMC article

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.

Figures

Figure 1.
Figure 1.
Publication, integration, and execution of applications with Boutiques.
Listing 1.
Listing 1.
Example of a Number-type input.
Listing 2.
Listing 2.
Example of an output leveraging path-template search-and-replacement.
Listing 3.
Listing 3.
Example of a configuration input file. The file template is defined as an array of strings to allow for multi-line strings in JSON.
Algorithm 1
Algorithm 1
Command-line construction
Listing 4.
Listing 4.
Excerpt from invocation schema showing dependencies between two mutually exclusive parameters num_input and str_input.
Listing 5.
Listing 5.
A minimal Boutiques descriptor.

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