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Co-Scientist CLI

Installation​

Command not found​

If you see seqera: command not found after installation:

  1. Verify the installation location:

    which seqera

  2. Ensure the npm global bin directory is in your PATH:

    # Check npm global bin directory
    npm bin -g

    # Restart your terminal or run
    source ~/.bashrc  # or ~/.zshrc

  3. If you installed the standalone binary, verify it is in a directory on your PATH:

    echo $PATH
npm permission errors​

If you encounter permission errors during installation:

  1. Use the npm prefix option to install to a user-writable directory:

    npm install -g seqera --prefix ~/.npm-global

  2. Add the directory to your PATH:

    export PATH="$HOME/.npm-global/bin:$PATH"
EACCES permission errors on global install​

Avoid running sudo npm install. Either fix npm permissions or install Node through a version manager such as nvm.

seqera: command not found after install​

Confirm npm's global bin directory is on your PATH. Run npm config get prefix to find it.

Authentication​

Browser doesn't open​

If the browser doesn't open automatically:

  1. Check the terminal output for a URL
  2. Copy and paste the URL into your browser manually
  3. Complete authentication in the browser
Login timeout​

If authentication times out:

  1. Ensure you have internet connectivity
  2. Check that https://seqera.io is accessible
  3. Log out and log in again
Token storage errors​

If you see errors related to credential storage:

  1. Check that you have write permissions to ~/.config/seqera-ai/

    ls -la ~/.config/seqera-ai/

  2. If the directory doesn't exist, create it:

    mkdir -p ~/.config/seqera-ai
Session expired​

If your session has expired:

  1. Log out and log in again:

    seqera logout
    seqera login
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