search

SegataLab / export2graphlan

Conversion software tool for producing both annotation and tree files for GraPhlAn
https://segatalab.github.io/tools/graphlan
MIT License
8 stars 6 forks source link

Python 3 compatibility #1

Closed Midnighter closed 4 years ago

Midnighter commented 4 years ago

Hi,

From your requirements list it is not immediately obvious why export2graphlan should be Python 2.7 only. Could you comment on that? I'd be happy to submit a patch that makes it 2&3 compatible.

fasnicar commented 4 years ago

Dear Moritz,

Many thanks for your offer, but the main restriction that ties export2graphlan to Python 2 is GraPhlAn. GraPhlAn has not yet been migrated to Python 3, so there is no point in having GraPhlAn and export2graphlan based on different Python versions at the moment.

Best, Francesco

Midnighter commented 4 years ago

Okay, that makes sense. I was asking because I'm actually trying to visualize some kraken2 output and convert the kraken output to BIOM format which I then convert with export2graphlan and it seems that the newer biom-format versions only support Python 3.

Since I run these as individual steps in a nextflow pipeline, having different Python versions for the data conversion and the image drawing later would not be a problem. That said, I now have a conda Python 2.7 environment with everything installed just fine. I previously tried with biocontainers and that was problematic.

jorondo1 commented 2 years ago

As of today I assume GraphLan is working since I managed to install it on python 3.9. Is export2graphlan now compatible as well? I am quite new to this, following the metaphlan tutorial both install don't work; however, graphlan did using $ git clone https://github.com/biobakery/graphlan.git

Thanks

fasnicar commented 2 years ago

Hi, we actually did not migrate export2graphlan to Python 3, while GraPhlAn is now Python 3 compatible, sorry about this. It is on our todo list, but not with a very high priority at the moment. If you could manage to get it running into a separate environment running Python 2.7 would be great. Otherwise, I'll try to give you a timeline about when we could be able to have it migrated as well.

Many thanks, Francesco

jorondo1 commented 2 years ago

thanks a lot for the quick reply. Running it on python 2.7 shouldn't be a problem. I would still be curious to know around when the migration would be done if you have any idea.

Cheers !