GNU Astronomy Utilities manual

4.2.4 System wide

When Gnuastro is installed, the configuration files that are shipped with the distribution are copied into the (possibly system wide) prefix/etc/ directory. See Configuring for more details on prefix (by default it is: /usr/local). This directory is the final place (with the lowest priority) that the programs in Gnuastro will check to retrieve parameter values.

If you remove a parameter and its value from the files in this system wide directory, you either have to specify it in more immediate configuration files or set it each time in the command line. Recall that none of the programs in Gnuastro keep any internal default values and will abort if they don’t find a value for the necessary parameters (except the number of threads). So even though you might never use a parameter, it still has to be at least available in this system-wide configuration file.

In case you install Gnuastro from your distribution’s repositories, prefix will either be set to / (the root directory) or /usr, so you can find the system wide configuration variables in /etc/ or /usr/etc/. The prefix of /usr/local/ is conventionally used for programs you install from source by your self.

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GNU Astronomy Utilities manual, November 2015.