Abstract
BackgroundTo 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.ResultsLog::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.AvailabilityThe source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).ConclusionUsing 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.
Highlights
To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run
We introduce here the module Log::ProgramInfo to facilitate run-time logging of Perlbased pipelines, thereby directly improving the reproducibility of modern bioinformatic analyses
The default name used for the log file includes the name of the program that is being reported upon as well as a timestamp to distinguish separate runs—you might choose to override the name or directory path to provide more complete organisation of logged results
Summary
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 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 Availability: The source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~ boutroslb/Log-ProgramInfo/)
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