How to properly run prokka on Ubuntu 22?

Question

[marongiu.luigi]

Hello

I have installed prokka on Ubuntu 22 with the command sudo apt -y install prokka. The installation seems complete but when I try to set the database I get the error:

$ prokka --setupdb
[19:13:28] Appending to PATH: /usr/bin
[19:13:28] Cleaning databases in /home/gigiux/.local/lib/prokka/db
[19:13:28] Cleaning complete.
[19:13:28] Looking for 'makeblastdb' - found /usr/bin/makeblastdb
[19:13:28] Determined makeblastdb version is 002012 from 'makeblastdb: 2.12.0+'
[19:13:28] Looking for 'hmmpress' - found /usr/bin/hmmpress
[19:13:28] Determined hmmpress version is 003003 from '# HMMER 3.3.2 (Nov 2020); http://hmmer.org/'
[19:13:28] Looking for 'cmpress' - found /usr/bin/cmpress
[19:13:28] Determined cmpress version is 001001 from '# INFERNAL 1.1.4 (Dec 2020)'
[19:13:28] Pressing CM database: /home/gigiux/.local/lib/prokka/db/cm/Viruses
[19:13:28] Running: cmpress \/home\/gigiux\/\.local\/lib\/prokka\/db\/cm\/Viruses

Error: File existence/permissions problem in trying to open CM file /home/gigiux/.local/lib/prokka/db/cm/Viruses.
CM file ~.local/lib/prokka/db/cm/Viruses not found (nor an .i1m binary of it)

[19:13:28] Could not run command: cmpress \/home\/gigiux\/\.local\/lib\/prokka\/db\/cm\/Viruses

What could be the error? Of course, it is due to the absence of the folder prokka inside /lib, since I don't have such a folder inside .local. Prokka is installed inside /usr/share. Why it is looking for .local then?

How to solve it?

Thank you

[Ram]

The instructions say these are the commands for Ubuntu:

sudo apt-get install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl
sudo cpan Bio::Perl
git clone https://github.com/tseemann/prokka.git $HOME/prokka
$HOME/prokka/bin/prokka --setupdb

Can you try these commands instead of the apt-get install you're doing?

[Ram]

It seems like prokka is creating a file under ~/.local/ so I don't think you need something there already. Also, the software itself might be wherever but ~/.local/lib/prokka/ is probably where it stores some sort of databases.