Are there any inclusion relationships between PhaGCN, PhaTYP, and PhaBOX software?

[ShuqingL]

Can the functions of the PhaGCN and PhaTYP software be achieved by using different functional modules in the PhaBOX software?

[KennthShang]

Sorry, I do not catch up with the idea.

Currently, both PhaGCN and PhaTYP can be run separately using PhaBOX, you can check this in the WIKI

Maybe you can further explain your needs.

Best,
Jiayu

[ShuqingL]

@KennthShang
Does this mean that in the future, using --task phagcn and --task phatyp of PhaBOX can respectively achieve the functions of PhaGCN and PhaTYP, without the need to use PhaGCN and PhaTYP separately?

[KennthShang]

@ShuqingL

The current version of PhaBOX can do this. The functions have already been released.

Also for your question, you can refer to the WIKI Installation. It is a closed issue and the mentioned problem has been fixed.

BTW, python>=3.8 should be fine. But I suggest installing a via BioConda.

Best,
Jiayu

[ShuqingL]

Thanks @KennthShang
But I received some warning messages when installing using Miniconda (Python version 3.9). I don't know if it's related to the Python version. Currently still under installation.

conda create -n phabox2 phabox=2.1.9 -c conda-forge -c bioconda -y

Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1., but conda is ignoring the . and treating it as 1.7.1 done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): | WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.8.0., but conda is ignoring the . and treating it as 1.8.0
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.6.0., but conda is ignoring the . and treating it as 1.6.0
WARNING conda.models.version:get_matcher(546): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.9.0., but conda is ignoring the . and treating it as 1.9.0 done
Solving environment: -

[KennthShang]

The WARNING information won't matter. It only tells you your conda version is out-of-date (in my opinion). Please provide the error message (if the installation failed)

[ShuqingL]

Hi @KennthShang,
Perhaps there are still compatibility issues with Python versions.
There has been no progress under Miniconda (Python version 3.9), and it got stuck at the step of "Solving environment: ".
After switching to Miniconda (Python version 3.8), the installation was completed smoothly.
I've successfully installed it now. Thank you very much.

[KennthShang]

Good to know.

I think it is caused by your conda version and I will release a note for that. Thanks for your feedback.

Best,
Jiayu