Hi Kenneth, Kenneth Hoste <kenneth.ho...@ugent.be> writes:
> Hi Loris, > > On 16/08/2019 14:50, Loris Bennett wrote: >> Hi, >> >> When I do >> >> $ module add BioPerl/1.7.2-foss-2018b-Perl-5.28.0 >> $ bp_genbank2gff3.pl -in test_in.gbff -out test_out.gff3 >> >> I get >> >> Can't locate YAML.pm in @INC (you may need to install the YAML module) >> (@INC contains: blib/lib /home/loris/bioperl-live >> /trinity/shared/easybuild/software/BioPerl/1.7.2-foss-2018b-Perl-5.28.0/lib/perl5/site_perl/5.28.0/x86_64-linux-thread-multi >> >> /trinity/shared/easybuild/software/BioPerl/1.7.2-foss-2018b-Perl-5.28.0/lib/perl5/site_perl/5.28.0 >> /trinity/shared/easybuild/software/BioPerl/1.7.2-foss-2018b-Perl-5.28.0 >> /trinity/shared/easybuild/software/XML-LibXML/2.0132-GCCcore-7.3.0-Perl-5.28.0/lib/perl5/site_perl/5.28.0/x86_64-linux-thread-multi >> >> /trinity/shared/easybuild/software/XML-LibXML/2.0132-GCCcore-7.3.0-Perl-5.28.0/lib/perl5/site_perl/5.28.0 >> >> /trinity/shared/easybuild/software/XML-LibXML/2.0132-GCCcore-7.3.0-Perl-5.28.0 >> /usr/local/share/perl5 >> /trinity/shared/easybuild/software/Perl/5.28.0-GCCcore-7.3.0/lib/perl5/site_perl/5.28.0/x86_64-linux-thread-multi >> >> /trinity/shared/easybuild/software/Perl/5.28.0-GCCcore-7.3.0/lib/perl5/site_perl/5.28.0 >> >> /trinity/shared/easybuild/software/Perl/5.28.0-GCCcore-7.3.0/lib/perl5/5.28.0/x86_64-linux-thread-multi >> >> /trinity/shared/easybuild/software/Perl/5.28.0-GCCcore-7.3.0/lib/perl5/5.28.0) >> at >> /trinity/shared/easybuild/software/BioPerl/1.7.2-foss-2018b-Perl-5.28.0/bin/bp_genbank2gff3.pl >> line 221. >> >> This seems to be because >> >> BioPerl-1.7.2-intel-2018b-Perl-5.28.0.eb >> >> depends, obviously, on Perl 5.28.0, but >> >> $ grep YAML Perl-5.28.0-GCCcore-7.3.0.eb >> ('YAML::Tiny', '1.73', { >> 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', >> >> whereas >> >> $ grep YAML Perl-5.28.1-GCCcore-8.2.0.eb >> ('YAML::Tiny', '1.73', { >> 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', >> ('YAML', '1.29', { >> 'source_tmpl': 'YAML-%(version)s.tar.gz', >> >> So is the YAML missing from the Perl 5.28.0 module or does BioPerl >> depend on the wrong Perl module, or is something else going on? > > Looks like YAML is indeed missing from the Perl 5.28.0 installation... > > It's easy to add that to the easyconfig though (and update your Perl > installation using "eb --force --skip", see > https://easybuild.readthedocs.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip). I add missing YAML module to Perl-5.28.0-GCCcore-7.3.0.eb and now all is well. Thank you. > We should also try and come up with a sanity check command to be added to > BioPerl, so we can avoid this in the future. > > Would something like "bp_genbank2gff3.pl --help" (or equivalent) work to catch > this issue? I think your suggestion is probably sufficient. Cheers, Loris -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de