could not open configuration file

yueli711 has asked for the wisdom of the Perl Monks concerning the following question:

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Re: could not open configuration file by haukex (Archbishop) on Jun 30, 2019 at 12:25 UTC
I think the error message is pretty self-explanatory. Some quick Googling shows that the "HOMER Installation Guide" describes that one should download configureHomer.pl, save it in the directory where you would like the software to be installed (such as `/home/username/homer`), and then run `perl /home/username/homer/configureHomer.pl -install`. It looks like that script writes the `config.txt` file.	[reply] [d/l] [select]
Re^2: could not open configuration file by yueli711 (Sexton) on Jun 30, 2019 at 16:38 UTC
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 $val in concatenation (.) or string at conf +igureHomer.pl line 599. [download]	[reply] [d/l]
Re^3: could not open configuration file by haukex (Archbishop) on Jun 30, 2019 at 16:49 UTC
`$ 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
Re: could not open configuration file by hippo (Bishop) on Jun 30, 2019 at 09:38 UTC
Some possibilities: You have forgotten to create/install the file `config.txt` You have created/installed the file `config.txt` but not at the path specified You have created/installed the file `config.txt` at the path specified but have given it the wrong permissions and/or contexts. Are you really running ./makeBigWig.pl as root and if so, why? You have mangled the installation of homer, whatever that is (the path does look rather unlikely) Note that this is basic debugging and not specific to Perl in any way.	[reply] [d/l] [select]
Re^2: could not open configuration file by yueli711 (Sexton) on Jun 30, 2019 at 16:33 UTC
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]	[reply] [d/l]
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
Re^4: could not open configuration file by yueli711 (Sexton) on Jun 30, 2019 at 16:56 UTC
Re^5: could not open configuration file by AnomalousMonk (Archbishop) on Jun 30, 2019 at 22:29 UTC
Re: could not open configuration file by Anonymous Monk on Jun 30, 2019 at 03:48 UTC
Link?	[reply]


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