Question: Homer error "findMotifsGenome.pl" : Can't locate HomerConfig.pm in @INC
0
gravatar for scheme4193
9 months ago by
scheme419370
scheme419370 wrote:

Hey everyone. I stuck an error when running homer script findMotifsGenome.pl .

The error content is like this.

Can't locate HomerConfig.pm in @INC (you may need to install the HomerConfig module)

BEGIN failed--compilation aborted at /path-to-homer-bin/findMotifsGenome.pl line 22.

From this error, I thought I failed to install homer properly, but I installed homer like this.

wget configureHomer.pl & perl configureHomer.pl -install & perl configureHomer.pl -install mm10

If anyone knows the solution, please let me know ! Thanks.

ADD COMMENTlink modified 9 months ago by Mensur Dlakic7.3k • written 9 months ago by scheme419370

Just a guess but I would remove these & since this sends all processes to background while starting them simultaneously. Install the basic Homer first, wait until finished properly, then install additional stuff like annotations for your organism. Do things sequentially but properly. If you want this sequentially this would be &&, not &. Still do it manually, typing in one command after the other and check the log messages for each step.

ADD REPLYlink modified 9 months ago • written 9 months ago by ATpoint42k
2
gravatar for Mensur Dlakic
9 months ago by
Mensur Dlakic7.3k
USA
Mensur Dlakic7.3k wrote:

The way you installed the program was most likely not system-wide. Just like shell needs the $PATH variable to know when to look for executable programs, perl needs to be told via $PERL5LIB variable where to look for modules. How to set this variable is explained here.

You can try to find HomerConfig.pm by typing locate HomerConfig.pm. If that actually gives you a directory where this module resides, that directory needs to be added to the $PERL5LIB variable. For most local installations, that would be either $HOME/perl/lib/perl5 or $HOME/perl/share/perl5. It is not a bad idea to add those two locations to $PERL5LIB no matter what.

PS If you have sudo privileges, you could reinstall the whole thing as root user and the modules will probably placed into a directory that is already included in $PERL5LIB.

ADD COMMENTlink modified 9 months ago • written 9 months ago by Mensur Dlakic7.3k
1

After fighting the error, I finally found the cause.

In findMotifsGenome.pl script, there are 2 lines in top of the file. use lib "/homer-directory/.//bin"; my $homeDir = "/homer-directory/./"; However, this homer-directory is set as compiled directory. After compiled homer, I move program directory, so is has changed.

Thank you for your comment !

ADD REPLYlink written 9 months ago by scheme419370

Would you mind giving a detailed step? I am a newbie and use conda. Thanks in advance.

ADD REPLYlink written 4 weeks ago by changshengw60
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