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
