BioMake：一个与 GNU make 兼容的用于声明式工作流管理的实用程序。
BioMake: a GNU make-compatible utility for declarative workflow management.
机构信息
Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
出版信息
Bioinformatics. 2017 Nov 1;33(21):3502-3504. doi: 10.1093/bioinformatics/btx306.
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.
动机
Unix 'make' 程序在生物信息学管道中被广泛使用，但存在一些限制其在大型分析数据集上应用的问题。这些问题包括依赖文件修改时间来确定目标是否过时、缺乏对集群上并行执行的支持，以及对底层逻辑程序的扩展的限制。
结果
我们提出了 BioMake，这是一个类似于 make 的实用程序，与大多数 GNU Make 的功能兼容，并添加了对流行的基于集群的作业队列引擎的支持、将 MD5 签名作为时间戳的替代，以及 Prolog 中的逻辑编程扩展。
可用性和实现
BioMake 可从 https://github.com/evoldoers/biomake 获得 MacOSX 和 Linux 系统，许可证为 BSD3。唯一的依赖项是 SWI-Prolog（版本 7），可从 http://www.swi-prolog.org/ 获取。
联系方式
ihholmes+biomake@gmail.com 或 cmungall+biomake@gmail.com。
补充信息
比较 BioMake 和类似工具的功能表。补充数据可在 Bioinformatics 在线获得。
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