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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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Pysam not found even after installing velocyto #327

Closed dajsfiles closed 4 months ago

dajsfiles commented 2 years ago

Hi,

I separately installed velocyto and pysam using conda, and both were successfully installed without issue. However, if I import velocyto in python, I get the following issue:

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
/tmp/817998.tmpdir/ipykernel_7316/2299111139.py in <module>
      1 import loompy
----> 2 import velocyto as vcy
      3 import scanpy.api as sc

~/.local/lib/python3.9/site-packages/velocyto/__init__.py in <module>
      8 from .molitem import Molitem
      9 from .logic import *
---> 10 from .counter import ExInCounter
     11 from .metadata import MetadataCollection, Metadata
     12 from .neighbors import BalancedKNN, convolve_by_sparse_weights

~/.local/lib/python3.9/site-packages/velocyto/counter.py in <module>
     12 import velocyto as vcy
     13 import h5py
---> 14 import pysam
     15 import numpy as np
     16 import os

ModuleNotFoundError: No module named 'pysam'

I've reinstalled pysam and velocyto several times, but the issue persists.