"ModuleNotFoundError: No module named 'genotoscope'"after installation

[jade0530]

Hi Developer,
We have those errors running gentoscope_annotate.py after git cloning the repository and installing all dependencies followed by instructions on wiki. Below are the details of the error:
Traceback (most recent call last):
File "genotoscope_annotate.py", line 6, in
from genotoscope.variants.AnnotateVariants import AnnotateVariants
ModuleNotFoundError: No module named 'genotoscope'

Can you provide some workaround to solve that?
Thanks,
Jade

[damianosmel]

Hi Jade,

First thanks for the question and the interest in the genotoscope.

About your question, please do the following steps and let me know what you see:

conda activate genotoscope_env
# check python version 
python --version
#shall give python 3.7.X (at my set-up X=12)
#navigate to the root path of genotoscope
cd ~/path/to/cloned-genotoscope-repo
ls 
# you shall see the following content:
# genotoscope       genotoscope_env_requirements.txt  LICENSE    toy_dataset
# genotoscope_data  genotoscope_local.yaml_           README.md  website_settings_server.ini_

#run the help for genotoscope_classify
python genotoscope/genotoscope_classify.py --help
# you shall see:
# INFO:hgvs:hgvs 1.5.1; released: True
# usage: genotoscope_classify.py [-h] [--analysis_root ANALYSIS_ROOT]
#                               [--input_variants INPUT_VARIANTS]
#                               [--output_path OUTPUT_PATH]
# ... rest omitted ...

The reason that you need to run from the root of the project is that genotoscope is a module (a folder containing a __init__.py) that is used throughout the project and in genotoscope_classify.py as well.

Let me know how it goes in your set-up,
Damianos