Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.

Q2 Decision Sciences Source Code for Biology and Medicine Pub Date : 2016-06-24 eCollection Date: 2016-01-01 DOI:10.1186/s13029-016-0055-9

John M Macdonald, Paul C Boutros

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Abstract

Background: To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.

Results: Log::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.

Availability: The source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).

Conclusion: Using Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research.

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Log::ProgramInfo：用于收集和记录生物信息学管道数据的 Perl 模块。

背景为了重现和报告生物信息学分析，确定程序的运行环境非常重要。当试图调试为什么不同的执行结果出乎意料地不同时，这也很有价值：Log::ProgramInfo是一个Perl模块，可在外层程序执行结束时写入日志文件，记录有用的执行特征。该日志文件可用于重新创建环境，以重现早期的执行情况。它还可用于比较两次执行的环境，以确定是否存在任何可能影响（或解释）其运行的差异：源代码可在 CPAN 上获取（Macdonald 和 Boutros，Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/）。结论：使用 Log::ProgramInfo 对程序的运行有很大帮助：在为可发表的研究创建结果数据的程序中使用 Log::ProgramInfo，并将 Log::ProgramInfo 输出日志作为该研究成果发表的一部分，是一种有价值的方法，可帮助他人复制编程环境，作为验证和/或扩展该研究的前奏。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Source Code for Biology and Medicine Decision Sciences-Information Systems and Management

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期刊介绍： Source Code for Biology and Medicine is a peer-reviewed open access, online journal that publishes articles on source code employed over a wide range of applications in biology and medicine. The journal"s aim is to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.

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