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skinniderlab / CLM

MIT License
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installation instructions #211

Closed skinnider closed 3 weeks ago

skinnider commented 4 weeks ago

I can't seem to follow the README at https://github.com/skinniderlab/CLM/blob/master/workflow/README.md on either della or argo. My code below:

argo

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/Genomics/skinniderlab/ms0270/conda/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/Genomics/skinniderlab/ms0270/conda/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/Genomics/skinniderlab/ms0270/conda/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/Genomics/skinniderlab/ms0270/conda/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

mkdir /Genomics/skinniderlab/PED-generation
cd /Genomics/skinniderlab/PED-generation

conda create --prefix /Genomics/skinniderlab/PED-generation/env-clm python=3.10 pip
conda activate /Genomics/skinniderlab/PED-generation/env-clm

cd ~/git/clm
pip install -e .[dev]

I get this error:

Obtaining file:///Genomics/skinniderlab/PED-generation
ERROR: file:///Genomics/skinniderlab/PED-generation does not appear to be a Python project: neither 'setup.py' nor 'pyproject.toml' found.

della:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/scratch/gpfs/SKINNIDER/ms0270/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/scratch/gpfs/SKINNIDER/ms0270/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/scratch/gpfs/SKINNIDER/ms0270/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/scratch/gpfs/SKINNIDER/ms0270/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

mkdir /scratch/gpfs/SKINNIDER/PED-generation
cd /scratch/gpfs/SKINNIDER/PED-generation

conda create --prefix /scratch/gpfs/SKINNIDER/PED-generation/env-clm python=3.10 pip
conda activate /scratch/gpfs/SKINNIDER/PED-generation/env-clm

cd ~/git/clm
pip install -e .[dev]

Same error:

Obtaining file:///scratch/gpfs/SKINNIDER/PED-generation
ERROR: file:///scratch/gpfs/SKINNIDER/PED-generation does not appear to be a Python project: neither 'setup.py' nor 'pyproject.toml' found.

I'm guessing that this has to do with installing the conda environment on the /scratch filesystem?

skinnider commented 3 weeks ago

cd ~/git/CLM ... 🤦‍♂️