kcleal / pywfa

Python wrapper for wavefront alignment using WFA2-lib
MIT License
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Colab - Import Error "undefined symbol: wavefront_align" #5

Closed AxelGiottonini closed 1 year ago

AxelGiottonini commented 1 year ago

Hello !

I tried running the Overview example on Colab. After installing successfully pywfa-0.4.1 with pip, I tried to import the WaveFrontAligner but the following error is raised:

ImportError                               Traceback (most recent call last)
<ipython-input-5-c314336c1681> in <module>
----> 1 import pywfa.align

/usr/local/lib/python3.9/dist-packages/pywfa/__init__.py in <module>
      1 from __future__ import absolute_import
----> 2 from .align import WavefrontAligner, clip_cigartuples, cigartuples_to_str, elide_mismatches_from_cigar
      3 

ImportError: /usr/local/lib/python3.9/dist-packages/pywfa/align.cpython-39-x86_64-linux-gnu.so: undefined symbol: `wavefront_align`

I will try to run the example locally but I would like to know if someone had the same issue or if there is a way to fix it ?

kcleal commented 1 year ago

Hi @AxelGiottonini, I've not tried Colab. Can you try installing with conda?

AxelGiottonini commented 1 year ago

Hey ! Thanks for the answer !

So I tried installing it with conda but it seems that pywfa is not compatible with the reste of my environment as it fails to install.

Also I tried installing it locally with pip but the same error appeared.

kcleal commented 1 year ago

Hopefully the pip install route should now be more reliable. Please open again if the issue persists.