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Open Access Highly Accessed Commentary

Ten recommendations for creating usable bioinformatics command line software

Torsten Seemann

GigaScience 2013, 2:15  doi:10.1186/2047-217X-2-15

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Some additional remarks

Gert Wollny   (2014-01-14 01:21)  Universidad Politechnica de Madrid

aproposThanks for this nice roundup. I'd like to add a few comments: In addition, to #2 I would suggest that it is always a good idea to add a Unix style man page that also shows a working example. On one hand, it helps to discover programs by using the apropos command, and on the other hand, seeing a working example greatly helps to get started. #7 can be quite challenging - especially if your software used dynamically loadable plug-ins and configuration files. As an alternative, I'd suggest to make the software installable in a system-specific way that takes care of setting up the path properly. In that context, when you work on Linux, and your software is free and open source, it is also a good idea to get the software included into the corresponding packaging system. Here one can also assure #9, i.e. that by installing the software package all its required dependencies are installed as well (especially, if they are also free software).

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