Issue with PHAROKKA 1.1.0 or 1.2.0 intsallation

[nicolasginet]

• phrokka version: 1.1.0
• Python version: 3.9
• Operating System: Unbuntu 20.04.2

Description

I am trying to install PHAROKKA from Github using conda or mamba. I tried on 3 different machines (1 MAC OS X and 2 PC running Ubuntu). And I always failed. I tried PHAROKKA 1.1.0 as well as 1.2.0. Databases do install properly but when I type the Help command pharroka.py -h I always get the following messages. Can you help me ?

Thanks
Nico

What I Did

Traceback (most recent call last):
  File "/home/julia/miniconda3/envs/pharokkaENV/bin/pharokka.py", line 5, in <module>
    import processes
  File "/home/julia/miniconda3/envs/pharokkaENV/bin/processes.py", line 8, in <module>
    from BCBio import GFF
  File "/home/julia/miniconda3/envs/pharokkaENV/lib/python3.9/site-packages/BCBio/GFF/__init__.py", line 3, in <module>
    from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple
  File "/home/julia/miniconda3/envs/pharokkaENV/lib/python3.9/site-packages/BCBio/GFF/GFFParser.py", line 34, in <module>
    from Bio.Seq import UnknownSeq
ImportError: cannot import name 'UnknownSeq' from 'Bio.Seq' (/home/julia/miniconda3/envs/pharokkaENV/lib/python3.9/site-packages/Bio/Seq.py)

[gbouras13]

Hi @magbphp ,

Thanks for pointing this out to me.

I think the error is with the new version 1.81 of biopython, specifically this issue.

Please reinstall pharokka as follows:

conda install pharokka biopython=1.80.

Which should fix the error. Let me know if it does not work.

I will change the environment and bioconda recipe as well.

George

[gbouras13]

This should now be fixed with v1.2.1 which is available on bioconda.

[bernt-matthias]

FYI: I guess it might have been a bit better to pin at bcbio-gff, like so bioconda/bioconda-recipes#39703 .. and pin the latest bcbio-gff version in the pharokka recipe .. but the additional pin on biopython at the pharokka recipe also should not hurt.

[gbouras13]

Thanks @bernt-matthias, I should probably just get rid of the dependency all together to be honest, maybe for the next version update when I get some time.

And thanks for your work in getting Pharokka onto Galaxy (presumably where this arose looking at the PR there) - I really appreciate it!

George