Re^2: could not open configuration file

Hello, haukex, Thank you for your response!

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 config
+ureHomer.pl
        i.e. save this in a directory named homer/ or something like t
+hat
    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 replacem
+ent of executables)

    Options:
        -list (prints available and installed packages to screen)
        -install (install basic Homer software from scratch)
        -install <package name1> [package name2] ... (installs package
+s)
        -version <version> (install specific version of package)
        -remove <package name1> [package name2] ... (safely removes pa
+ckages)
        -update (updates all packages to the newest version)
        -reinstall (forces the reinstallation of all currently install
+ed packages)
        -all (install everything - will take a while...)
        -getFacts (add humor to HOMER - to remove delete contents of d
+ata/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 change
+s 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 confi
+g.txt if upgrading):
            -bigWigUrl <base urls for bigWigs> (Setting for makeBigWig
+s.pl)
            -bigWigDir <base directory for bigWigs> (Setting for makeB
+igWigs.pl)
            -hubsUrl <base urls for hubs> (Setting for makeMultiWigHub
+.pl)
            -hubsDir <base directory for hubs> (Setting for makeMultiW
+igHub.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 -big
+WigDir

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

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

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

    Updating Settings...
Use of uninitialized value $val in concatenation (.) or string at conf
+igureHomer.pl line 599.
[download]

Comment on Re^2: could not open configuration file Download Code

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Re^3: could not open configuration file by haukex (Archbishop) on Jun 30, 2019 at 16:49 UTC
`$ 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?	[reply] [d/l] [select]
Re^4: could not open configuration file by yueli711 (Sexton) on Jun 30, 2019 at 17:02 UTC
Hello, haukex, Thank you so much for your response. I tried to use makeBigWig.pl to transfer thefile to bigwig and I can visualize it in UCSC browser. Following is the protocol. Thank you again for your great help! Yue Li `To make bigWig files easier to generate, HOMER includes a program crea +tively named "makeBigWig.pl" that automates all of the steps below. makeBigWig.pl <tag directory> <genome> [special options] [makeUCSC fil +e options] -webDir /path-to-web-fold/ -url http://webserverURL/bigwig +Fold/ i.e. makeBigWig.pl PU.1-ChIP-Seq/ mm9 -webDir /var/www/bigWigs/ -url +http://ChuckNorrisU.edu/bigWigs/` [download]	[reply] [d/l]


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