-configuration file instead. We look for a file named \(dq.htsnrc\(dq
-in the user's home directory; its syntax is given by examples in the
-htsnrc.example file (included with \fBhtsn\fR).
+configuration file instead. We first look for \(dqhtsnrc\(dq in the
+system configuration directory. We then look for a file named
+\(dq.htsnrc\(dq in the user's home directory. The latter will override
+the former.
+.P
+The user's home directory is simply $HOME on Unix; on Windows its
+wherever %APPDATA% points. The system configuration directory is
+determined by Cabal; the \(dqsysconfdir\(dq parameter during the
+\(dqconfigure\(dq step is used.