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franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
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CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. #106

Closed tan-yuwei closed 2 years ago

tan-yuwei commented 2 years ago

Dear Francisco,

Hi! :)

I tried to run a commond {bash metaGEM.sh -t check}, it returned as below:

Setting current directory to root in config.yaml file ...

Checking if conda is available ... detected version 4.12.0! Searching for metaGEM conda environment ... detected! Activating metagem env ...

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

Searching for metaWRAP conda environment ... detected! Searching for prokka-roary conda environment ... detected!

Could you tell me how can I properly configured shell? Many thanks in advance!

Best, Yuwei

franciscozorrilla commented 2 years ago

Hi Yuwei,

I encourage you to set up & use metaGEM on your university's high performance computer cluster (HPC), instead of trying to install on your local machine. Your university's HPC will likely have conda installed as a loadable module, so you would not run into this problem when using metaGEM as described in the methods section of the paper.

This issue has more to do with setting up conda on your local machine rather than with metaGEM itself, so please refer to google search + the conda documentation to learn how to set up conda on your machine. It looks like the solution to your question is in the error message you posted:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'. To initialize your shell, run

$ conda init

Currently supported shells are:

  • bash
  • fish
  • tcsh
  • xonsh
  • zsh
  • powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

e.g. if you have a mac try conda init zsh Happy to help with any questions more specifically related to metaGEM.

Best, Francisco

tan-yuwei commented 2 years ago

Hi Francisco,

Many thanks for your reply. Your response helpled me a lot.

Best regards, Yuwei

franciscozorrilla commented 2 years ago

No problem, good luck with your analysis!