Python dependent library installation troubleshooting

velocyto

If you failed CellOracle installation because of velocyto installation error, please try to install velocyto using the following commands or please follow the author’s instruction .

conda install numpy scipy cython numba matplotlib scikit-learn h5py click pysam llvm louvain

Then

pip install velocyto

Some MacOS users have encountered compiler errors during the installation of velocyto. Several different errors have been reported. You may find the solution for each of these in the links below.

scanpy

If you failed CellOracle installation because of Scanpy installation error, please try to install Scanpy using the following commands or the author’s instruction .

conda install scanpy

pybedtools

If you have an error related to the pybedtools installation, please install pybedtools using anaconda.

conda install -c bioconda pybedtools

Note

Pybedtools is python wrapper of bedtools. If you get “NotImplementedError” during ATAC-seq peak processing step, please try to install bedtools.

sudo apt-get install bedtools

Install gimmemotifs with conda

If you failed installation in the gimmemotifs installation step, please install gimmemotifs solely first. We recommend installing gimmemotifs using conda prior to celloracle installation.

conda install -c bioconda gimmemotifs

Note

If your jupyter notebook kernel keep dying during TF motif scan, there are mainly two possibilities below.

  1. Your kernel might be killed because of memory shortage. Please make sure you have enough memory.

2. If you have enough memory, there is most likely a problem with the gimmemotifs installation in your environment. Please uninstall gimmemotifs and re-install gimmemotifs using conda.

pip uninstall gimmemotifs -y
conda install -c bioconda gimmemotifs

Warning

We found gimmemotifs might have installation issue with anaconda bioconda channel (at 7/7/2022). If you fail to install gimmemotifs with anaconda, we recommend installing it using anaconda’s offline mode. More information can be found here.