Open lskatz opened 3 years ago
Hi, I faced the same Bioperl version error with prokka v1.14.5 (which I installed using Conda) and the run was aborted. Prokka v1.14.6 (installed from source) still shows the error as a warning, but it runs the code and doesn't abort. I guess the code has changed. Not sure what _prokkaversion you are using.
_Here's how I solved it on v1.14.5:_
Need this module.
use Perl::Version;
Changed the code a bit on those specific lines (starts from line 259)
my $minbpver = "1.006002"; # for Bio::SearchIO::hmmer3
my $bpver0 = Perl::Version->new($Bio::Root::Version::VERSION);
my $bpver = $bpver0->numify;
msg("You have BioPerl $bpver");
err("Please install BioPerl $minbpver or higher") if $bpver < $minbpver;
Prokka checks for bioperl >=
1.0006002
numerically using this code on line 257.However when you have bioperl v1.7.8, it returns the semver 3-integer notation like
Therefore it will exit because the comparison will compare
1.006002 < 1.7.8
. I am not sure what the correct fix is yet but I am willing to look it up if you would accept a pull request.