[bug] pin bioperl version in Prokka module

[rpetit3]

The latest version of Bioperl is causing some issues with Prokka. (See related issue: https://github.com/tseemann/prokka/issues/598)

  Bio::SearchIO: hmmer3 cannot be found
  Exception
  ------------- EXCEPTION -------------
  MSG: Failed to load module Bio::SearchIO::hmmer3. Can't locate Bio/SearchIO/hmmer3.pm in @INC (you may need to install the Bio::SearchIO::hmmer3 module) (@INC contains: /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/5.32/site_perl /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/site_perl /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/5.32/vendor_perl /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/vendor_perl /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/5.32/core_perl /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/core_perl .) at /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/site_perl/Bio/Root/Root.pm line 520.

  STACK Bio::Root::Root::_load_module /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/site_perl/Bio/Root/Root.pm:522
  STACK (eval) /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/site_perl/Bio/SearchIO.pm:620
  STACK Bio::SearchIO::_load_format_module /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/site_perl/Bio/SearchIO.pm:619
  STACK Bio::SearchIO::new /opt/bactopia/envs/bioconda--prokka-1.14.6/lib/perl5/site_perl/Bio/SearchIO.pm:217
  STACK toplevel /opt/bactopia/envs/bioconda--prokka-1.14.6/bin/prokka:1113
  -------------------------------------


  For more information about the SearchIO system please see the SearchIO docs.
  This includes ways of checking for formats at compile time, not run time
  Can't call method "next_result" on an undefined value at /opt/bactopia/envs/bioconda--prokka-1.14.6/bin/prokka line 1114.

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Closes #XXX

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[jfy133]

@rpetit3 how does the bug affect the singularity/docker containers?

[rpetit3]

I got this fixed on the bioconda side, so will just need to change the docker and singularity build number

https://github.com/bioconda/bioconda-recipes/pull/33411

[rpetit3]

Slightly annoying difference between conda and mamba

conda is getting prokka 1.14.6 pl5321hdfd78af_2 (causes bioperl v1.7.8 which does not work with Prokka) mamba is getting prokka 1.14.6 pl5262hdfd78af_3 (fix with bioperl pinned to v1.7.2)

I'm going to wait some time to see if it conda starts picking up the latest build, otherwise bioperl will need to be pinned

[rpetit3]

Great, just waiting on singularity image availability

[ramprasadn]

singularity image is available now 😄