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bioinfo-chru-strasbourg / howard

Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery
GNU Affero General Public License v3.0
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Potential Python Version Dependency Issue (Resolved) #238

Closed judefelixt closed 4 months ago

judefelixt commented 5 months ago

I encountered challenges using Howard due to the Python version in my development environment. Here's a breakdown:

Python 3.12.3: The installation of Howard failed due to conflicts within its dependencies, particulary related to the pandas library. Python 3.10.0: While Howard installed successfully with this version, I faced errors when processing .gz files. Python 3.10.13 (Success!): Using Python 3.10.13 resolved both installation and processing issues, allowing me to work with Howard seamlessly.

bioinfo-chru-strasbourg commented 5 months ago

Dear @judefelixt,

HOWARD was tested with Python 3.10.x versions, but not with 3.12.x.

First of all, I was not able to reproduce the error when processing .gz file with version 3.10.0. Can you explain in detail your test?

For Python version 3.12.3, installation seems to fail:

Failed to build bgzip duckdb pyarrow pysam

Moreover, HOWARD was not tested with 3.11.x version.

So, I suggest to unsure version 3.10.x to install and use HOWARD. Use conda like this:

conda create -n howard python=3.10
conda activate howard
pip install -e .
howard --help
conda deactivate
antonylebechec commented 4 months ago

Some fixes and python release check