homer makebigwig error

Question

[yueli7]

Hello,

I have already installed homer, and tried to use makeBigWig.pl.

Thanks in advance for any help!

With Best,

Yue Li

            Unzipping...
    Finished Installing homer

root@ACB-HuangLab-Ubuntu:/home/administrator/homer# ./makeBigWig.pl
Could not open configuration file (/Applications/commandline/Homer/.//config.txt)

[ATpoint]

How is it that the executable is in /home while the config.txt is is /Applications. Please share the install command.

[yueli7]

Hello, ATpoint,

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 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.

[ATpoint]

Ok but still, how does config makes it way to /Applications. I suggest removing everything towards homer from the entire system and rerun the installer or try to make a symbolic link from the actual config file to the path indicated above.

[yueli7]

Hello, ATpoint,

Thank you so much for your help!

Yue

nano ~/.bash_profile
PAH=$PATH:/home/administrator/homer/bin


File Name to Write: /home/administrator/.bash_profile                           
^G Get Help         M-D DOS Format      M-A Append          M-B Backup File
^C Cancel           M-M Mac Format      M-P Prepend

Which I can make choise?

Thank you so much!

Yue Li

[ATpoint]

I don't understand the question. There is a typo PAH => PATH

[yueli7]

administrator@ACB-HuangLab-Ubuntu:~$ nano ~/.bash_profile
administrator@ACB-HuangLab-Ubuntu:~$ source ~/.bash_profile
administrator@ACB-HuangLab-Ubuntu:~$ cd homer
administrator@ACB-HuangLab-Ubuntu:~/homer$ findMotifs.pl
Can't locate Statistics.pm in @INC (you may need to install the Statistics module) (@INC contains: /Applications/commandline/Homer/.//bin /gpfs/data01/cbenner/software/homer/.//bin /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /home/administrator/homer/bin/findMotifs.pl line 24.
BEGIN failed--compilation aborted at /home/administrator/homer/bin/findMotifs.pl line 24.

[yueli7]

Hello ATpoint,

Thank you so much for your time!

Yue

Answer 1

[ATpoint]

Look, I think you are massively messing up things by using paths from different posts such as Homer error, how to call homer properly in a script? and how to know that it's actually working. You are on Linux so /Applications should not even be present by default, this is a Mac folder. Go and delete everything related from Homer from your machine, every folder, file and script. Then download the recent installer script, check you have all dependencies installed as instructed on the Homer website. If there are perl modules missing, install them. Maybe get a recent perl version via the anaconda package manager. Do all that and then see what happens. Also remove everything from bashrc/_profile that was Homer-related.