Can't locate COMMON.pm in @INC - The-Bioinformatics-Group/Albiorix GitHub Wiki

This error message means that Perl is unable to find the Perl module COMMON.pm in its include path (@INC). COMMON.pm is part of Trinity's own Perl library, and Perl can not access this library by default.

To solve this problem, you need to edit the file "~/.bashrc". This can be done by opening the file with a text editor of your choice. You could for example use the text editor nano by typing the following in the command line:

nano ~/.bashrc

To the ~/.bashrc file, add the following line:

export PERL5LIB=/usr/local/opt/perl/lib/site_perl/5.14.2:/usr/local/bin/trinityrnaseq_r20140717/PerlLib

This line will enable Perl to find and use the Trinity library.

Also, if there isn't already a line like that in your ~/.bashrc file, add:

export PATH=$PATH:/usr/local/bin

After you've done this, save the changes to the file and run the following command:

source ~/.bashrc

Note: Make sure that you run the "source" command in the screen where you are going to run Trinity, and after logging in using qlogin. Otherwise, it might not work.

Now, Trinity should be working.

If it still doesn't work, you could try to add the following line to the ~/.bashrc file as well:

alias perl='/usr/local/opt/perl/bin/perl'

This line will specify the version of Perl that will be used.