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kundajelab / bpnet

Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
http://bit.ly/bpnet-colab
MIT License
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Error building Leidenalg wheel in Colab environment #44

Open cmboye opened 2 years ago

cmboye commented 2 years ago

Hello,

I am a graduate student from the Luca/Pique-Regi lab and I'm trying to install leidenalg to ultimately run BPNet. I am using a Google Colab environment with Python 3.6. Please see below:

!sudo apt-get install build-essential autoconf automake flex bison
!sudo update-alternatives --config python3
!sudo apt install python3-pip
!python -m pip install --upgrade pip
!apt-get install -y bedtools > /dev/null
!pip install pprint -i http://pypi.douban.com/simple/ --trusted-host pypi.douban.com
!pip install git+https://github.com/kundajelab/DeepExplain.git --quiet
!pip install -U cloudpickle<1.7.0 h5py tqdm --quiet
!pip install -U pyyaml --quiet
!pip install igraph
!pip install leidenalg --no-use-pep517
!export DISABLE_BCOLZ_AVX2=true
!pip install bpnet --quiet --quiet

I get the following error: ERROR: Failed building wheel for leidenalg. Do you know what might cause this? I do not think I will be able to use a different version of Python due to errors with other dependencies. Thank you!