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gtonkinhill / panaroo

An updated pipeline for pangenome investigation
MIT License
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Biopython deprecation error #301

Open lucyjanekelly opened 1 month ago

lucyjanekelly commented 1 month ago

I have tried to install panaroo on an HPC cluster using conda as well as manually. I have python 3.9 loaded into my environment. However, no matter how I install it, when I try to use panaroo it gives this error:

"BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules.

We instead now recommend building your command line and invoking it directly with the subprocess module."

Biopython's website says it deprecated python 3.9, but it still has the same error when I tried with a newer python version. I also don't know how to build my command line and invoke it directly with the subprocess module.

gtonkinhill commented 1 month ago

Hi,

This appears to be just a warning at the moment. We are in the process of removing the Bio.Application module as it has been deprecated.

However, it should still be present within BioPython, and thus Panaroo should continue to run for now after printing this warning.

Stellar427 commented 1 month ago

Hi,

Thanks for creating panaroo

I installed the tool via mamba .when I try to use panaroo it gives this error:

python3.11/site-packages/Bio/Application/init.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.

Due to the on going maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules.

We instead now recommend building your command line and invoking it directly with the subprocess module. warnings.warn( Need specified aligner to be installed