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a-h-b / dadasnake

Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
GNU General Public License v3.0
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error: "Could not create conda environment from ... " #27

Closed gljessen closed 2 years ago

gljessen commented 2 years ago

Hey there, (problem) (Mac OS) having an error after step 6 of the Dadasnake tutorial; "Initialize conda environments: This run sets up the conda environments that will be usable by all users:"

when running: ./dadasnake -i config/config.init.yaml

I get the following error message: Initializing conda environments. CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. To initialize your shell, run

Then runs and crashes into: CreateCondaEnvironmentException: Could not create conda environment from /Users/.....

I have tried reinstalling everything and removing environments, also changing shell conda init bash or conda init zsh but the error persists. Moreover, a new set of "Encountered problems while solving:" appeared each time.

Thanks!

Screenshot: image

pommesjet commented 2 years ago

Try navigating to the folder and manually deleting the tensorflow-gpu folder then try again

gljessen commented 2 years ago

That doesn't makes any sense

a-h-b commented 2 years ago

Hi - it's possible that it just doesn't install on Mac, because the conda packages don't always all work on mac. Give me a couple of days to check, if I can find versions that do. But yeah, if you've got a linux machine, that would solve it. Best wishes - AHB

gljessen commented 2 years ago

Hi - it's possible that it just doesn't install on Mac, because the conda packages don't always all work on mac. Give me a couple of days to check, if I can find versions that do. But yeah, if you've got a linux machine, that would solve it. Best wishes - AHB

much appreciated

a-h-b commented 2 years ago

Hi - I've had a look, but I also can't seem to get the conda installations to work on mac. Do you have access to a linux machine? -AHB

gljessen commented 2 years ago

Thank you, yes at the end I'm working on the server only. Thanks again!