update PERL5LIB for ubuntu

[lskatz]

Hi, when I install something like bioperl using apt-get install, it sends the libraries outside of PERL5LIB, to /usr/share/perl5. Could you update PERL5LIB to include that? My "patch" is this step, right after the step with shogo82148/actions-setup-perl@v1.

      - name: initial envs
        run:  |
          echo "PERL5LIB=$PERL5LIB:/usr/share/perl5" >> $GITHUB_ENV

[tobyink]

apt-get is always going to install modules into library paths of the system Perl (which I think is Perl 5.30 on the ubuntu-latest platform). In general, two copies of Perl with different minor version numbers (e.g. 5.28.0 and 5.30.0) cannot share library dirs. It may "work" in some cases, but will fail spectacularly in others — especially anything that uses XS.

Why not use cpanm BioPerl to install BioPerl instead of using apt-get?

If you set things up with local::lib, you can even install BioPerl (and other modules) somewhere in your $HOME and then cache it between runs, so it doesn't need reinstalling every time.

[lskatz]

You might be right. And really excellent point about XS modules. I went with apt because BioPerl is a beast to install and I think that they optimize the speed of installation somehow on the ubuntu package. However I should probably do it the right way through cpanm.

[tobyink]

Installing it through apt-get, it will download an already-compiled version, so yeah, will be much faster. But actions/cache@v2 can help with that. And besides, it's GitHub's CPU cycles anyway. :D