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).
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?
regards,
Kenneth
