`qiime tools view` on headless server

User Support
2

Hi @steviep, This issue is related to the headless server issue from before. qiime tools view uses the registered system application to open the visualization index (e.g. index.html -> web browser, index.pdf -> pdf viewer, index.txt -> text editor). Without a desktop environment, qiime has no way of handling the request to open the visualization (you don’t have any applications to view it with!). I have opened up a bug report/feature request here — we will make sure that the failure notice is more meaningful, and will suggest alternatives for viewing visualizations in reduced/headless environments.

For now, you have a few options:

  • Transfer the artifacts to your local workstation using SFTP/SCP/etc:

    # On your local machine:
$ scp -i /path/to/identity_file.pem \
    user@qiime-server:/path/to/viz.qzv \
    /local/path/where/we/should/put/the/viz.qzv

  • open the artifact using https://view.qiime2.org

  • install qiime2 locally (you only need qiime2 and q2cli), and run qiime tools view there

  • Upgrade your Ubuntu 16.04 installation from a server install to a desktop install. You will need to Google around about how to do this, but last time I did something similar it looked like: sudo apt-get update && sudo apt-get install ubuntu-desktop. Once upgraded you would need to do something like X forwarding or set up a VNC connection to log in graphically. YMMV.

Personally I would go with the file transfer option, and use https://view.qiime2.org! Hope that helps!

3 Likes