Problem with installing prokka

[NorthonColt]

I'm trying to install prokka on a linux server with the following specifications:

• Python version 3.11.7
• Perl version 5.38.2
• OS: Rocky Linux 8.9 (Green Obsidian)

For the installation I tried to use the specified command using conda:
conda install -c conda-forge -c bioconda -c defaults prokka
However, after running this code, and trying to check the version of the installed prokka (prokka -version) I get the error attached in prokka_install_error.txt.
prokka_install_error.txt

Thank you in advance for your help, it is very much appreciated.

Best regards,
Márton Réit

[m-abdullah-nabeel]

Hi @NorthonColt!
As the error clearly shows you may need to install the Bio::Root::Version module, you are probably missing bioperl as one the dependencies.

1. You may try to install bioperl manually as written in the docs of bioperl at https://github.com/bioperl/bioperl-live/blob/master/README.md#installation
2. Since you are already using conda, make sure you have activated the correct environment having all the dependies in it. You can also try installing bioperl via conda conda install -c bioconda bioperl.
3. Further make sure the all the installed dependencies are added to PATH. You can try which command for this purpose. Like which python3 etc.
4. Finally, after checking all the dependencies are installed, try to reinstall according to the docs mentioned at https://github.com/tseemann/prokka#installation for your relevant environment. Or try to force re-install conda install -c conda-forge -c bioconda -c defaults --force-reinstall prokka.
   In a nutshell, I think either you are missing the dependencies or they are not really added to the path.