run agat_convert_sp_gff2gtf.pl after conda install

[nbisweden]

run agat_convert_sp_gff2gtf.pl after conda install

[Juke34]

did you create the environment and install agat properly before?

conda create -n agat
conda activate agat
conda install -c bioconda agat

then the command would be
agat_convert_sp_gff2gtf.pl --gff file.gff -o file.gtf no need to precise perl

[Diango700]

yes like ;
conda create --name agat

but same error

[Juke34]

Ok you have a Conda env called agat
step1 you have created it with the command
conda create --name agat
and step2 activated it with the command
conda activate agat

But the error message says that prerequisites (e.g Sort/Naturally.pm) is not installed while they are supposed to be installed by conda. So apparently either you forgot the step3 in which you have to install agat conda install -c bioconda agat either during this installation conda threw an error message...

It seems you did a clone of the repo and try to run directly the script without having installed any prerequisite.

[Diango700]

I try to re-install

[Diango700]

thank you so much Juke34 !
its ok now