Re: could not open configuration file

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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
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]