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in linux command line. I run these series of lines:

source /Path/To/Tools/For/Conda/Env
conda load miniconda/3
conda activate special
snakemake --core 1

This works great!

When I turn this into a shell, it doesnt work and I dont understand why...

#!/bin/bash

source /Path/To/Tools/For/Conda/Env
conda load miniconda/3
conda activate special
snakemake --core 1

I get this error: _conda_EXE= /Path/To/Tools/For/bin/Conda/Env Command not found

_conda_ROOT= /Path/To/Tools/For Command not found

Badly placed ()'s

CommandNotFoundError: your shell has not been propertly configured to use conda activate. if you shell is bash or bourne variant, enable conda for current use with

$ echo ". /Path/To/Tools/For/Conda/Env" >> ~/.bashrc

I am kind of new at this want to fix this, how?

Genetics
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    See duplicate, specifically [this answer is good](https://stackoverflow.com/a/58081608/570918). Also, changing the shebang can be sufficient: `#!/bin/bash -l` – merv Jan 05 '22 at 01:23
  • @ merv, thank you for this. I was googling around alot yesterday and didnt see this post. This was very helpful! – Genetics Jan 05 '22 at 16:35

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