administrator@ACB-HuangLab-Ubuntu:~/homer$ perl configureHomer.pl

	Current base directory for HOMER is /home/administrator/homer/./


	Usage: configureHomer.pl [options]
	This program will install HOMER in the directory containing configureHomer.pl
		i.e. save this in a directory named homer/ or something like that
	To install the program from scratch, run the following command:
		perl path-to-homer/configureHomer.pl -install
	If upgrading, make sure HOMER is not running (may prevent replacement of executables)

	Options:
		-list (prints available and installed packages to screen)
		-install (install basic Homer software from scratch)
		-install <package name1> [package name2] ... (installs packages)
		-version <version> (install specific version of package)
		-remove <package name1> [package name2] ... (safely removes packages)
		-update (updates all packages to the newest version)
		-reinstall (forces the reinstallation of all currently installed packages)
		-all (install everything - will take a while...)
		-getFacts (add humor to HOMER - to remove delete contents of data/misc/)
		-check (checks for required 3rd party software)
		-make (reconfigure files, recompile exectables)
		-sun (Use with SunOS - i.e. gmake and gtar instead of make and tar)
		-keepScript (do NOT replace configureHomer.pl script if changes are detected with website)
		-url <installation url> (For use if the Homer website changes)
			default is: http://homer.ucsd.edu/homer/
		Hubs & BigWig settings (with read existing settings from config.txt if upgrading):
			-bigWigUrl <base urls for bigWigs> (Setting for makeBigWigs.pl)
			-bigWigDir <base directory for bigWigs> (Setting for makeBigWigs.pl)
			-hubsUrl <base urls for hubs> (Setting for makeMultiWigHub.pl)
			-hubsDir <base directory for hubs> (Setting for makeMultiWigHub.pl)
	Configuration files: downloads update.txt from the homer website,
		and corrects config.txt with the appropriate options

administrator@ACB-HuangLab-Ubuntu:~/homer$ perl configureHomer.pl -bigWigDir

	Current base directory for HOMER is /home/administrator/homer/./

	Updating Settings...
Use of uninitialized value $val in concatenation (.) or string at configureHomer.pl line 599.
administrator@ACB-HuangLab-Ubuntu:~/homer$ perl configureHomer.pl -bigWigUrl

	Current base directory for HOMER is /home/administrator/homer/./

	Updating Settings...
Use of uninitialized value $val in concatenation (.) or string at configureHomer.pl line 599.