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BioShake: a Haskell EDSL for bioinformatics workflows

Typical bioinformatics analyses comprise of long running computational workflows. An important part of reproducible research is the management and execution of these workflows to allow robust execution and to minimise errors. BioShake is an embedded domain specific language in Haskell for specifying...

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Detalles Bibliográficos
Autor principal: Bedő, Justin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6625497/
https://www.ncbi.nlm.nih.gov/pubmed/31328031
http://dx.doi.org/10.7717/peerj.7223
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author Bedő, Justin
author_facet Bedő, Justin
author_sort Bedő, Justin
collection PubMed
description Typical bioinformatics analyses comprise of long running computational workflows. An important part of reproducible research is the management and execution of these workflows to allow robust execution and to minimise errors. BioShake is an embedded domain specific language in Haskell for specifying and executing computational workflows for bioinformatics that significantly reduces the possibility of errors occurring. Unlike other workflow frameworks, BioShake raises many properties to the type level allowing the correctness of a workflow to be statically checked during compilation, catching errors before any lengthy execution process. BioShake builds on the Shake build tool to provide robust dependency tracking, parallel execution, reporting, and resumption capabilities. Finally, BioShake abstracts execution so that jobs can either be executed directly or submitted to a cluster. BioShake is available at http://github.com/PapenfussLab/bioshake.
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spelling pubmed-66254972019-07-19 BioShake: a Haskell EDSL for bioinformatics workflows Bedő, Justin PeerJ Bioinformatics Typical bioinformatics analyses comprise of long running computational workflows. An important part of reproducible research is the management and execution of these workflows to allow robust execution and to minimise errors. BioShake is an embedded domain specific language in Haskell for specifying and executing computational workflows for bioinformatics that significantly reduces the possibility of errors occurring. Unlike other workflow frameworks, BioShake raises many properties to the type level allowing the correctness of a workflow to be statically checked during compilation, catching errors before any lengthy execution process. BioShake builds on the Shake build tool to provide robust dependency tracking, parallel execution, reporting, and resumption capabilities. Finally, BioShake abstracts execution so that jobs can either be executed directly or submitted to a cluster. BioShake is available at http://github.com/PapenfussLab/bioshake. PeerJ Inc. 2019-07-09 /pmc/articles/PMC6625497/ /pubmed/31328031 http://dx.doi.org/10.7717/peerj.7223 Text en ©2019 Bedő http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Bedő, Justin
BioShake: a Haskell EDSL for bioinformatics workflows
title BioShake: a Haskell EDSL for bioinformatics workflows
title_full BioShake: a Haskell EDSL for bioinformatics workflows
title_fullStr BioShake: a Haskell EDSL for bioinformatics workflows
title_full_unstemmed BioShake: a Haskell EDSL for bioinformatics workflows
title_short BioShake: a Haskell EDSL for bioinformatics workflows
title_sort bioshake: a haskell edsl for bioinformatics workflows
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6625497/
https://www.ncbi.nlm.nih.gov/pubmed/31328031
http://dx.doi.org/10.7717/peerj.7223
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