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KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
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Installation error #29

Closed swvanderlaan closed 6 months ago

swvanderlaan commented 7 months ago

I have a conda-environment with python 3.8.18 and tried to install your tool as per instruction. 

pip install -e .
Obtaining file:///Users/slaan3/git/Monopogen
  Preparing metadata (setup.py) ... done
Collecting pandas>=1.2.3 (from Monopogen==1.0.0)
  Using cached pandas-2.0.3-cp38-cp38-macosx_10_9_x86_64.whl.metadata (18 kB)
Requirement already satisfied: pysam>=0.16.0.1 in /Users/slaan3/miniconda3/envs/scqtl/lib/python3.8/site-packages (from Monopogen==1.0.0) (0.22.0)
Requirement already satisfied: NumPy>=1.19.5 in /Users/slaan3/miniconda3/envs/scqtl/lib/python3.8/site-packages (from Monopogen==1.0.0) (1.24.4)
Requirement already satisfied: sciPy>=1.6.3 in /Users/slaan3/miniconda3/envs/scqtl/lib/python3.8/site-packages (from Monopogen==1.0.0) (1.10.1)
Requirement already satisfied: pillow>=8.2.0 in /Users/slaan3/miniconda3/envs/scqtl/lib/python3.8/site-packages (from Monopogen==1.0.0) (10.1.0)
Requirement already satisfied: python-dateutil>=2.8.2 in /Users/slaan3/miniconda3/envs/scqtl/lib/python3.8/site-packages (from pandas>=1.2.3->Monopogen==1.0.0) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /Users/slaan3/miniconda3/envs/scqtl/lib/python3.8/site-packages (from pandas>=1.2.3->Monopogen==1.0.0) (2023.3.post1)
Requirement already satisfied: tzdata>=2022.1 in /Users/slaan3/miniconda3/envs/scqtl/lib/python3.8/site-packages (from pandas>=1.2.3->Monopogen==1.0.0) (2023.3)
Requirement already satisfied: six>=1.5 in /Users/slaan3/miniconda3/envs/scqtl/lib/python3.8/site-packages (from python-dateutil>=2.8.2->pandas>=1.2.3->Monopogen==1.0.0) (1.16.0)
Using cached pandas-2.0.3-cp38-cp38-macosx_10_9_x86_64.whl (11.7 MB)
Installing collected packages: pandas, Monopogen
  Attempting uninstall: pandas
    Found existing installation: pandas 0.25.3
    Uninstalling pandas-0.25.3:
      Successfully uninstalled pandas-0.25.3
  Attempting uninstall: Monopogen
    Found existing installation: Monopogen 1.0.0
    Uninstalling Monopogen-1.0.0:
      Successfully uninstalled Monopogen-1.0.0
  Running setup.py develop for Monopogen
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
genometools 0.4.1 requires pandas<1,>=0.20.1, but you have pandas 2.0.3 which is incompatible.
Successfully installed Monopogen-1.0.0 pandas-2.0.3

How can I fix this error? Or is it inconsequential?

jinzhuangdou commented 7 months ago

It seems you have genometools 0.4.1 installed leading to conflict on some packages. Maybe you can setup a new conda environment for Monopogen install?