BRAKER - Genome annotation, software error ?

Question

[sunnykevin97]

Hi,

Try to run BRAKER after installing all the dependencies, unable to run couldn't really understand the error.

In-addition I installed the Scalar::Util::Numeric perl module.

Suggestions please.

./braker.pl
Can't locate Scalar/Util/Numeric.pm in @INC (you may need to install the Scalar::Util::Numeric module) (@INC contains: /home/sun/perl5/lib/perl5/x86_64-linux-thread-multi /home/sun/perl5/lib/perl5 /home/sun/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/sun/anaconda3/lib/site_perl/5.26.2 /home/sun/anaconda3/lib/5.26.2/x86_64-linux-thread-multi /home/sun/anaconda3/lib/5.26.2 .) at ./braker.pl line 26.
BEGIN failed--compilation aborted at ./braker.pl line 26.

line 26 in braker.pl

 use Scalar::Util::Numeric qw(isint)

Answer 1

[Mensur Dlakic]

I will take your word that you installed the Scalar::Util::Numeric module, but it must be installed in a non-standard location. The contents of the @INC are telling you where the system is looking for perl modules (for you that would be /home/sun/perl5/lib/perl5/x86_64-linux-thread-multi /home/sun/perl5/lib/perl5 /home/sun/anaconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/sun/anaconda3/lib/site_perl/5.26.2 /home/sun/anaconda3/lib/5.26.2/x86_64-linux-thread-multi /home/sun/anaconda3/lib/5.26.2 directories). Most likely you will need to add a location of the installed Scalar::Util::Numeric module to the @INC variable, or force its installation into one of these directories that are already in the list.

https://perlmaven.com/how-to-change-inc-to-find-perl-modules-in-non-standard-locations

[sunnykevin97]

I resolved using conda.

[maja-lobermeier]

May I ask how? I have the same problem

[Ram]

bioconda has braker 1 2 and 3. Resolve it like you would resolve any other software installation using conda.