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. 2017 Nov 1;33(21):3502-3504.
doi: 10.1093/bioinformatics/btx306.

BioMake: a GNU make-compatible utility for declarative workflow management

Ian H Holmes  1   2 , Christopher J Mungall  3
Affiliations

BioMake: a GNU make-compatible utility for declarative workflow management

Ian H Holmes et al. Bioinformatics. .

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 modification 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.

Availability and implementation: BioMake is available for MacOSX and Linux systems from https://github.com/evoldoers/biomake under the BSD3 license. The only dependency is SWI-Prolog (version 7), available from http://www.swi-prolog.org/.

Contact: ihholmes + biomake@gmail.com or cmungall + biomake@gmail.com.

Supplementary information: Feature table comparing BioMake to similar tools. Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1
Fig. 1
A hypothetical BioMake Makefile that runs align on all ordered pairs of files mouse.fa, human.fa and zebrafish.fa. The rule for file align-$X-$Y creates an alignment (using the program align, assumed to exist on the user’s PATH) from any two files $X.fa and $Y.fa. However, it only applied for those $X and $Y which are flagged as being valid species, via the Prolog facts sp(X) which appear between prolog and endprolog directives. The top-level target all uses BioMake’s $(bagof…) function, a wrapper for the Prolog predicate bagof/3, to find all ordered pairs of species that match the rule. This example is dissected in the repository’s README.md
See this image and copyright information in PMC

References

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    1. Mungall CJ. (2009) Experiences using logic programming in bioinformatics. In P. M. Hill and D. S. Warren, editors, 25th International Conference on Logic Programming, volume 5649 of Lecture Notes in Computer Science, pages 1–21, Pasadena, CA, USA. Springer. DOI 10.1007/978-3-642-02846-5, ISBN 978-3-642-02846-5

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