Issue installing/running cellbender: No module named 'cellbender.remove_background'

Dear cellbender team!

I installed cellbender without error in a conda environment following the instructions, but when even trying to run any command with “cellbender,” I get the following error below. I have tried running this on a server with GPUs. Any help would be greatly appreciated!

Traceback (most recent call last):
  File "/home/chanj3/anaconda3/envs/cellbender/bin/cellbender", line 8, in <module>
    sys.exit(main())
  File "/home/chanj3/anaconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/base_cli.py", line 90, in main
    parser = get_populated_argparser()
  File "/home/chanj3/anaconda3/envs/cellbender/lib/python3.7/site-packages/cellbender/base_cli.py", line 76, in get_populated_argparser
    module_argparse = importlib.import_module('.'.join(module_argparse_str_list))
  File "/home/chanj3/anaconda3/envs/cellbender/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 953, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 965, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'cellbender.remove_background'

[jmchan88]

Ahh figured it out! I lied, I didn’t follow the directions exactly. I ran

pip install git+https://github.com/broadinstitute/CellBender.git

rather than actually cloning the github repository directly. I figured that it was going to be the same thing, but I guess not! Thanks!

[sjfleming]

Glad you got it to work!