Re^2: could not open configuration file

Hello, hippo, Thank you so much 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.
[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 16:35 UTC
As I said here, and as the output you showed says as well, did you ever try running it with `-install`?	[reply] [d/l]
Re^4: could not open configuration file by yueli711 (Sexton) on Jun 30, 2019 at 16:41 UTC
Hello, haukex, Thank you so much for your great help! administrator@ACB-HuangLab-Ubuntu:~/homer$ perl configureHomer.pl -ins +tall Current base directory for HOMER is /home/administrator/homer/./ --2019-06-30 08:39:34-- http://homer.ucsd.edu/homer/update.txt Resolving homer.ucsd.edu (homer.ucsd.edu)... 169.228.63.226 Connecting to homer.ucsd.edu (homer.ucsd.edu)\|169.228.63.226\|:80... co +nnected. HTTP request sent, awaiting response... 200 OK Length: 16187 (16K) [text/plain] Saving to: ‘/home/administrator/homer/.//update.txt’ 100%[================================================================> +] 16,187 --.-K/s in 0.05s 2019-06-30 08:39:34 (293 KB/s) - ‘/home/administrator/homer/.//update. +txt’ saved [16187/16187] Updating Settings... `wget -O 0.133731155962781.tmp http://homer.ucsd.edu/homer/configureHo +mer.pl`; --2019-06-30 08:39:34-- http://homer.ucsd.edu/homer/configureHomer.pl Resolving homer.ucsd.edu (homer.ucsd.edu)... 169.228.63.226 Connecting to homer.ucsd.edu (homer.ucsd.edu)\|169.228.63.226\|:80... co +nnected. HTTP request sent, awaiting response... 200 OK Length: 26485 (26K) [application/x-perl] Saving to: ‘0.133731155962781.tmp’ 100%[================================================================> +] 26,485 --.-K/s in 0.06s 2019-06-30 08:39:34 (467 KB/s) - ‘0.133731155962781.tmp’ saved [26485/ +26485] configureHomer.pl script is up-to-date Packages to Install... homer -> Checking for standard utilities and 3rd party software: (Note: seqlogo, gs, and blat no longer required) Checking for wget... /usr/bin/wget Checking for cut... /usr/bin/cut Checking for gcc... /usr/bin/gcc Checking for g++... /usr/bin/g++ Checking for zip... /usr/bin/zip Checking for unzip... /usr/bin/unzip Checking for make... /usr/bin/make Checking for tar... /bin/tar Checking for gunzip... /bin/gunzip Checking for gzip... /bin/gzip All auxilary programs found. Installing: homer Downloading... --2019-06-30 08:39:34-- http://homer.ucsd.edu/homer/data/software/hom +er.v4.10.4.zip Resolving homer.ucsd.edu (homer.ucsd.edu)... 169.228.63.226 Connecting to homer.ucsd.edu (homer.ucsd.edu)\|169.228.63.226\|:80... co +nnected. HTTP request sent, awaiting response... 200 OK Length: 35758069 (34M) [application/zip] Saving to: ‘homer.package.zip’ 100%[================================================================> +] 35,758,069 31.6MB/s in 1.1s 2019-06-30 08:39:36 (31.6 MB/s) - ‘homer.package.zip’ saved [35758069/ +35758069] Unzipping... Finished Installing homer 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 $val in concatenation (.) or string at conf +igureHomer.pl line 599. administrator@ACB-HuangLab-Ubuntu:~/homer$ perl configureHomer.pl -big +WigDir Current base directory for HOMER is /home/administrator/homer/./ Updating Settings... Use of uninitialized value $val in concatenation (.) or string at conf +igureHomer.pl line 599. administrator@ACB-HuangLab-Ubuntu:~/homer$ [download]	[reply] [d/l]
Re^4: could not open configuration file by yueli711 (Sexton) on Jun 30, 2019 at 16:56 UTC
Hello haukex, Thank you so much for your great help! administrator@ACB-HuangLab-Ubuntu:~/homer$ perl configureHomer.pl -ins +tall Current base directory for HOMER is /home/administrator/homer/./ --2019-06-30 08:39:34-- http://homer.ucsd.edu/homer/update.txt Resolving homer.ucsd.edu (homer.ucsd.edu)... 169.228.63.226 Connecting to homer.ucsd.edu (homer.ucsd.edu)\|169.228.63.226\|:80... co +nnected. HTTP request sent, awaiting response... 200 OK Length: 16187 (16K) [text/plain] Saving to: ‘/home/administrator/homer/.//update.txt’ 100%[================================================================> +] 16,187 --.-K/s in 0.05s 2019-06-30 08:39:34 (293 KB/s) - ‘/home/administrator/homer/.//update. +txt’ saved [16187/16187] Updating Settings... `wget -O 0.133731155962781.tmp http://homer.ucsd.edu/homer/configureHo +mer.pl`; --2019-06-30 08:39:34-- http://homer.ucsd.edu/homer/configureHomer.pl Resolving homer.ucsd.edu (homer.ucsd.edu)... 169.228.63.226 Connecting to homer.ucsd.edu (homer.ucsd.edu)\|169.228.63.226\|:80... co +nnected. HTTP request sent, awaiting response... 200 OK Length: 26485 (26K) [application/x-perl] Saving to: ‘0.133731155962781.tmp’ 100%[================================================================> +] 26,485 --.-K/s in 0.06s 2019-06-30 08:39:34 (467 KB/s) - ‘0.133731155962781.tmp’ saved [26485/ +26485] configureHomer.pl script is up-to-date Packages to Install... homer -> Checking for standard utilities and 3rd party software: (Note: seqlogo, gs, and blat no longer required) Checking for wget... /usr/bin/wget Checking for cut... /usr/bin/cut Checking for gcc... /usr/bin/gcc Checking for g++... /usr/bin/g++ Checking for zip... /usr/bin/zip Checking for unzip... /usr/bin/unzip Checking for make... /usr/bin/make Checking for tar... /bin/tar Checking for gunzip... /bin/gunzip Checking for gzip... /bin/gzip All auxilary programs found. Installing: homer Downloading... --2019-06-30 08:39:34-- http://homer.ucsd.edu/homer/data/software/hom +er.v4.10.4.zip Resolving homer.ucsd.edu (homer.ucsd.edu)... 169.228.63.226 Connecting to homer.ucsd.edu (homer.ucsd.edu)\|169.228.63.226\|:80... co +nnected. HTTP request sent, awaiting response... 200 OK Length: 35758069 (34M) [application/zip] Saving to: ‘homer.package.zip’ 100%[================================================================> +] 35,758,069 31.6MB/s in 1.1s 2019-06-30 08:39:36 (31.6 MB/s) - ‘homer.package.zip’ saved [35758069/ +35758069] Unzipping... Finished Installing homer 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 $val in concatenation (.) or string at conf +igureHomer.pl line 599. administrator@ACB-HuangLab-Ubuntu:~/homer$ perl configureHomer.pl -big +WigDir Current base directory for HOMER is /home/administrator/homer/./ Updating Settings... Use of uninitialized value $val in concatenation (.) or string at conf +igureHomer.pl line 599. administrator@ACB-HuangLab-Ubuntu:~/homer$ ./makeBigWig.pl Could not open configuration file (/Applications/commandline/Homer/.// +config.txt) [download]	[reply] [d/l]
Re^5: could not open configuration file by AnomalousMonk (Archbishop) on Jun 30, 2019 at 22:29 UTC
NB: Re^4: could not open configuration file differs from Re^4: could not open configuration file (immediately previous post) in the last two lines only! Give a man a fish: `<%-{-{-{-<`	[reply] [d/l]