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gao-lab / GLUE

Graph-linked unified embedding for single-cell multi-omics data integration
MIT License
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Unable to install on windows 10 #95

Closed Khalid-Usman closed 1 year ago

Khalid-Usman commented 1 year ago

I have created a new conda environment with python 3.10 and then run the following commands on Windows OS, but failed to install scglue.

conda install -c conda-forge -c bioconda scglue

or

pip install scglue

Getting the following error, 

FileNotFoundError: [WinError 2] The system cannot find the file specified
      # pysam: no cython available - using pre-compiled C
      # pysam: htslib mode is shared
      # pysam: HTSLIB_CONFIGURE_OPTIONS=None
      # pysam: htslib configure options: None
Jeff1995 commented 1 year ago

Hi @Khalid-Usman! Sorry for the late reply.

I'm afraid scglue doesn't support installing on Windows because it's dependency pybedtools, which subsequently depends on bedtools and htslib, does not support Windows. My suggestion would be to use a Linux machine or WSL.

Please let me know if there were further issues.