All the steps worked pretty well except the last line for database indexing $HOME/prokka/bin/prokka --setupdb
I got this compilation error message:
Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /home/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/miniconda3/lib/site_perl/5.26.2 /home/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/miniconda3/lib/5.26.2 .) at /home/prokka/bin/prokka line 29.
BEGIN failed--compilation aborted at /home/prokka/bin/prokka line 29.
You have multiple Perl installations which is causing your problem. You have a system Perl into which you have installed some Perl modules with sudo apt-get install. However, you also have a Miniconda installed Perl which is used by Prokka because it takes precedence in your path. Check out which -a perl that gives you a list of all Perl binaries in your Path. To solve this you need to decide which Perl you want to use. You could, for example, install all required modules using conda or cpan (checkout which cpan to see that you are using the conda-provisioned one), modify your $PATH environment to give precedence to system perl, or change all your perl scripts to start with #!/path/to/perl where path/to/perl is of course the path to the perl you choose. I do however recommend the first option to use conda perl.
Have you run
cpan install XML::Simplewith
sudo? It may have installed the module to your local path and that path may not be in your perl path. Try either adding that local directory to your perl path or installing the package with sudo.
Thanks for your comment, but
sudo cpan install XML::Simpledid not work!