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- Title
BioMake: a GNU make-compatible utility for declarative workflow management.
- Authors
Holmes, Ian H.; Mungall, Christopher J.
- Abstract
Motivation: The Unix 'make' program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modifi- cation times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program. Results: We present BioMake, a make-like utility that is compatible with most features of GNU Make and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog.
- Subjects
R (Computer program language); WORKFLOW management; BIOINFORMATICS software; LOGIC programming; PROLOG (Computer program language)
- Publication
Bioinformatics, 2017, Vol 33, Issue 21, p3502
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btx306