Open jianwu1 opened 1 month ago
I had a similar issue, but I managed to get CellOracle installed by modifying the compiler.
To be more precise, I removed the original gimmemotifs via pip uninstall gimmemotifs
It's possible that gfortran (a compiler for the Fortran language) is being used as a C compiler because it's more fault-tolerant for certain code or has better support for certain extensions. Even though it's not a compiler for C/C++ code, it might be able to handle code that standard C/C++ compilers can't handle correctly.
CC=/usr/local/bin/gfortran pip install gimmemotifs
CC=/usr/local/bin/gfortran pip install celloracle
finally,Celloracle is installed.
(For_sc) lironghai@lironghaideMacBook-Pro ~ % pip show celloracle
Name: celloracle
Version: 0.18.0
Summary: in silico gene perturbation analysis and GRN analysis with single cell data
Home-page: https://github.com/morris-lab/CellOracle
Author: Kenji Kamimoto
Author-email: kamimoto@wustl.edu
License: Apache License Version 2.0
Location: /Users/lironghai/anaconda3/envs/For_sc/lib/python3.10/site-packages
Requires: anndata, cython, genomepy, gimmemotifs, goatools, h5py, igraph, joblib, jupyter, louvain, matplotlib, numba, numpy, pandas, pyarrow, scanpy, scikit-learn, scipy, seaborn, tqdm, umap-learn, velocyto
Required-by:
This is the same method used for Velocyto to install.
CC=/usr/local/bin/gfortran pip install velocyto
operating system
Darwin lironghaideMacBook-Pro.local 23.5.0 Darwin Kernel Version 23.5.0: Wed May 1 20:19:05 PDT 2024; root:xnu-10063.121.3~5/RELEASE_ARM64_T8112 arm64
Python 3.10.8
numpy 2.0.0
pysam 0.22.1
Cython 3.0.10
Hi I've been trying to install celloracle on a macOS osx-64 conda environment but kept failing due to failing to build gimmemotifs:
But I have gimmemotifs installed by running
mamba install gimmemotifs
and you can see it's working:It seems celloracle during building is not detecting gimmemotifs but tries to build it again and fails. How can I fix this issue?