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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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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PeerJ Inc.
2019
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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. |
format | Online Article Text |
id | pubmed-6625497 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT bedojustin bioshakeahaskelledslforbioinformaticsworkflows |