$ perl configureHomer.pl -bigWigDir

I'm pretty sure that's not how you're supposed to use it, according to the documentation and the soruce, -bigWigDir should be followed by a new URL. You're getting the "Use of uninitialized value" warning because of the missing argument. But why run this command at all - maybe just try using the default settings first?

In reply to Re^3: could not open configuration file by haukex
in thread could not open configuration file by yueli711

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