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jaumlrc / ProphET

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GFFFile module #38

Open mariemh23 opened 5 years ago

mariemh23 commented 5 years ago

Hello,

I'm trying to use the "gff_rewrite.pl" to modify my gff generated by Prokka. I receive this error despite having installed all the necessary perl modules.

Can't locate GFFFile.pm in @INC (you may need to install the GFFFile module) (@INC contains: /home/mariemh/App/cgview_comparison_tool/lib/bioperl-1.2.3 /home/mariemh/App/cgview_comparison_tool/lib/perl_modules /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at gff_rewrite.pl line 13.

Could you help me install this module. I don't find it anywhere. ?

Thanks

jaumlrc commented 5 years ago

Hello Mariemh23

Thank you for using ProphET.

You can obtain the full GFFLib from:

https://github.com/gustavo11/GFFLib

However, ProphET download these libraries and scripts during the installation, and store them in the folder:

/UTILS.dir/GFFLib Please check if this folder was created, with the corresponding libraries and scripts. Another possible problem is that maybe the libraries are installed but are not in your @INC. You could try to add the libraries to the path manually: export PERL5LIB=/UTILS.dir/GFFLib Hope it helps! Enjoy ProphET! All my best, João Luís Reis Cunha Laboratório de Imunologia e Genômica de Parasitos Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Em qui, 5 de set de 2019 às 06:38, mariemh23 escreveu: > Hello, > > I'm trying to use the "gff_rewrite.pl" to modify my gff generated by > Prokka. I receive this error despite having installed all the necessary > perl modules. > > Can't locate GFFFile.pm in @inc (you may need to > install the GFFFile module) (@inc contains: > /home/mariemh/App/cgview_comparison_tool/lib/bioperl-1.2.3 > /home/mariemh/App/cgview_comparison_tool/lib/perl_modules /etc/perl > /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 > /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 > /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 > /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at > gff_rewrite.pl line 13. > > Could you help me install this module. I don't find it anywhere. ? > > Thanks > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > , > or mute the thread > > . >
mariemh23 commented 5 years ago

Thanks a lot @jaumlrc . It worked for me :)

tseemann commented 5 years ago

Wow, bioperl 1.2.3 is from 16 years ago!