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Co-Scientist

When installing or authenticating the Seqera CLI, or working with projects, you might encounter the following issues.

Installation​

seqera: command not found​

If you see seqera: command not found after installation:

  1. Verify the Seqera CLI installation location:

    which seqera

  2. Ensure the npm global bin directory is on your PATH. Find it with npm config get prefix or npm bin -g:

    # Check the 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.

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.
  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, log out and log in again:

seqera logout
seqera login

Projects​

Dataset uploads do not auto-attach the project label​

When you upload a dataset into a project, the project's proj_* label is not attached automatically.

This issue occurs when a pipeline carries a proj_* label that was not created in workspace settings. Co-Scientist still surfaces the project, inferred from the pipeline, but the project has no Platform-assigned label ID. Auto-attach requires that ID.

To avoid this issue, create proj_* labels in workspace settings before applying them to resources. See Projects.

No projects configured yet​

The Projects page shows a No projects configured yet empty state, the project selector is hidden, and the workspace view shows only its header.

This issue occurs when the workspace has no proj_* labels.

To resolve, ask a workspace admin to create the first proj_* label for the workspace. See Create a project.

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