Error in running metaGEM.sh

[Poccia]

After installing the pipeline through the manual installation guide (which worked better for me than the automatic installation), I was receiving the following error when trying the check with bash metaGEM.sh -t check:

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

Checking if conda is available ... detected version 4.13.0!
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:
  - 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'.


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

However, the problem seemed to be on the script, because I was able to execute conda activate normally. The source of the problem was on line 114 in metaGEM.sh, when the script calls conda activate metagem.

To solve this issue, first is important that you can call metagem env using conda activate metagem without the directly path to the env. I believe the best solution is to add the env directory locate inside metaGEM directory to the conda envs_dirs list with

conda config --append envs_dirs ~/metaGEM/envs

Then, to make sure the script will be able to use conda activate, following https://github.com/conda/conda/issues/7980#issuecomment-441358406, I add source ~/anaconda3/etc/profile.d/conda.sh to the top of the metaGEM.sh script, just after #!/bin/bash. This made the script works perfectly.