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bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
88 stars 18 forks source link

Error install Poppunk #211

Closed OrsonMM closed 2 years ago

OrsonMM commented 2 years ago

I have: These error

$ python3 poppunk-runner.py

Traceback (most recent call last): File "poppunk-runner.py", line 7, in from PopPUNK.main import main File "/home/administrador/programas/PopPUNK/PopPUNK/main.py", line 16, in import poppunk_refine ModuleNotFoundError: No module named 'poppunk_refine'

nickjcroucher commented 2 years ago

@OrsonMM please use the issue template and tell us how you installed PopPUNK.

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Command used and output returned

Describe the bug

aspitaleri commented 2 years ago

Hi - got identical error and I fixed as follow: After cloning the git, running python3 poppunk-runner.py it does not work (no module named "poppunk_refine". You need to build/install first using setup.py. I have install all dependencies, including cython and pybind11. In my Ubuntu I needed to export the path: export pybind11_DIR=/usr/local/lib/python3.8/dist-packages/pybind11/share/cmake/pybind11/

Finally, run

python setup.py build sudo python setup.py install

Then python poppunk-runner.py or just type poppunk works fine!

johnlees commented 2 years ago

Thanks @aspitaleri

This would work, or you can also install via conda. pip installation is temporarily unsupported.