During the creation of the virtual environment
# Make virtual env
conda create -n dev_genoml2 python=3.9
conda activate dev_genoml2
# Install GenoML to this
pip install umap-learn
pip install .
# Run step 1
genoml discrete supervised munge \
--prefix /Users/makariousmb/Documents/GitHub/dev_genoml2/outputs/test_discrete_geno \
--geno /Users/makariousmb/Documents/GitHub/dev_genoml2/examples/discrete/training \
--pheno /Users/makariousmb/Documents/GitHub/dev_genoml2/examples/discrete/training_pheno.csv
pip install . on windows machine Anaconda Terminal causes error "python setup.py egg_info did not run successfully." This is related to a charmap decoding error in the README.md file. The specific lines in setup.py that cause this error are
with open("README.md", "r") as fh: long_description = fh.read()
Commenting out these lines (21 and 22) and related lines 31 and 32 resolves this issue and allows pip install . to function properly
During the creation of the virtual environment
# Make virtual envconda create -n dev_genoml2 python=3.9conda activate dev_genoml2# Install GenoML to thispip install umap-learnpip install .# Run step 1genoml discrete supervised munge \--prefix /Users/makariousmb/Documents/GitHub/dev_genoml2/outputs/test_discrete_geno \--geno /Users/makariousmb/Documents/GitHub/dev_genoml2/examples/discrete/training \--pheno /Users/makariousmb/Documents/GitHub/dev_genoml2/examples/discrete/training_pheno.csvpip install .on windows machine Anaconda Terminal causes error "python setup.py egg_info did not run successfully." This is related to a charmap decoding error in the README.md file. The specific lines in setup.py that cause this error arewith open("README.md", "r") as fh: long_description = fh.read()Commenting out these lines (21 and 22) and related lines 31 and 32 resolves this issue and allows
pip install .to function properly