Ten recommendations for creating usable bioinformatics command line software

GigaScience

Torsten Seemann¹ 

[1]Victorian Bioinformatics Consortium, Building 76 Monash University Clayton, Clayton, VIC 3800, Australia

关键词: Tools;    Unix;    User interface;    Software quality;    Bioinformatics software;   

Others  :  861511
DOI  :  10.1186/2047-217X-2-15

 received in 2013-10-21, accepted in 2013-11-11,  发布年份 2013

【 摘 要 】

Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user’s time, and improve the quality of scientific analyses.

【 授权许可】

   
2013 Seemann; licensee BioMed Central Ltd.

【 参考文献 】

• [1]POSIX standards for command line interfaces http://www.gnu.org/prep/standards/html_node/Command_002dLine-Interfaces.html webcite
• [2]Wikipedia: getopt http://en.wikipedia.org/wiki/Getopt webcite
• [3]Galaxy tool shed http://wiki.galaxyproject.org/Tool%20Shed webcite
• [4]GitHub http://github.com webcite
• [5]Exit and exit status http://tldp.org/LDP/abs/html/exit-status.html webcite
• [6]Perl core modules: FindBin http://perldoc.perl.org/FindBin.html webcite
• [7]SAMtools http://samtools.sourceforge.net webcite