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stacy-l / snakemake_workshop

CCB Skills Seminar (Fall 2023) - snakemake
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snakemake command encounters error #1

Open deepmind11 opened 7 months ago

deepmind11 commented 7 months ago

My System: MacBook Pro M3; I am running a zsh terminal (also tried the below code in bash)

Here are the commands I ran on my local system

git clone https://github.com/ccbskillssem/snakemake_fa23.git conda env create --file envs/snakemake_fa23.yml conda activate snakemake_fa23

But I am getting the following error when running: snakemake -pj10 --use-conda output/visuals/vcf_heatmap.pdf -np

Screenshot 2024-02-15 at 8 52 42 PM

If I understood it properly, the below seems to be the main issue. I am unable to debug it.

/bin/bash: conda: command not found

I have conda already installed and in my PATH. ❯ conda --version conda 23.11.0

TIA.

(Coming here from YouTube, great lecture!)

stacy-l commented 5 months ago

Oh my god, I'm so sorry I haven't responded to this! If you never resolved this, please let me know and I'll see what I can do.