installation issue

[alessiaartusi]

Hi everybody,

I am having an issue installing PROKKA, the error message is the following: Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module)

[reaset41]

I am having the same issue. Were you able to resolve it?

[jessicalumian]

This seems to be a similar issue to https://github.com/tseemann/prokka/issues/446 which indiates a that bioperl is not installed. I think the conda installation of prokka is supposed to do this, but it also didn't work for me when I ran the conda install in the readme.

I fixed this by installing bioperl with the following command:

 conda install -c bioconda perl-bioperl 

For reference, all of my commands:

# command from readme
conda install -c conda-forge -c bioconda -c defaults prokka

# install bioperl
 conda install -c bioconda perl-bioperl 

After this I was able to run prokka.

[ambi1999]

Hi @jessicalumian ,

I am getting the same issue. Tried your method of 'conda install -c bioconda perl-bioperl ' but error persists. I am trying to install Prokka on 'Ubuntu 22.04 LTS'.

Can't locate Bio/Root/Version.pm in @INC (you may need to install the Bio::Root::Version module)

Thanks, Ambi.

[ChooseelBunsuwansakul]

Hi @jessicalumian, it doesn't work.

[mmcguffi]

I also run into this issue -- I dont know much about Perl, but I also encountered this problem using Roary and found a solution in their Github Issues

tldr; This solved it for me: export PERL5LIB=$CONDA_PREFIX/lib/perl5/site_perl/5.22.0/

My Perl version is v5.32.1 so Im not entirely sure why I have the directory to begin with, but it does solve the issue for me at least.

I believe this also relates to #446

[whipkreme]

Hi. can anyone help? im having this error while installing prokka.

Collecting package metadata (current_repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source. Collecting package metadata (repodata.json): done Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

[sterrettJD]

@whipkreme Are you trying to install it on a Mac with M1/M2 chip (ARM architecture)? I was having this issue on my Mac that was resolved when I used CONDA_SUBDIR=osx-64 conda create -n prokka_env, instead of conda create -n prokka_env.

See more info on conda environments with ARM architecture here.