Re: [easybuild] Perl YAML module missing as dependency for BioPerl?

[Kenneth Hoste]

On 21/08/2019 09:49, Loris Bennett wrote:
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.

Thanks for the feedback, we'll get this fixed in the next EasyBuild 
release too, see 
https://github.com/easybuilders/easybuild-easyconfigs/pull/8806 .



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.

Tried this myself, seems like --help exits with a non-zero exit code, so 
it's useless as a sanity check command anyway...


regards,

Kenneth