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?
Cheers,
Loris
--
Dr. Loris Bennett (Mr.)
ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
