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theislab / dca

Deep count autoencoder for denoising scRNA-seq data
Apache License 2.0
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Error in running dca #22

Closed nhuhoa closed 3 years ago

nhuhoa commented 5 years ago

Dear Gökçen,

I have installed dca using anaconda but when I try to run dca, there is a problem of import keras from dca. Anaconda installation of dca: conda install -c bioconda dca All setup conditions are the same as setup.py file. I use jupyter notebook and check the version of packages: scanpy==1.4 anndata==0.6.18 numpy==1.15.4 scipy==1.2.1 pandas==0.24.1 scikit-learn==0.20.2 statsmodels==0.9.0 python-igraph==0.7.1 louvain==0.6.1 keras== 2.0.8, six== 1.12.0, h5py== 2.9.0, kopt== 0.1.0

I can work with scanpy without any problem. However, when I import dca in Jupyter server using: from dca.api import dca they throw an error like this:

from keras.engine.base_layer import InputSpecModuleNotFoundError: No module named 'keras.engine.base_layer'

Have you ever met this case? Do you have any suggestions? Thanks a lot and nice day,

Best, Hoa Tran

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gokceneraslan commented 3 years ago

Should be fixed in the latest release.