Thanks for the responses. The suggested approach about adding a line to the matplotlibrc solved the problem. “qiime info” now shows the installed plugins. (see below). In a possibly related issue I was verifying the environment by working through the Moving Pictures tutorial which works until I attempt to view something. For example when I try to view demux-qual-plots.qzv I get the following error. I’m guessing that this will start a web browser (?) to read the index.html created in a subdirectory of /tmp although I can’t find evidence of the file ever being created. Just that it can’t open it. Thanks for your advice. I checked /var/log for evidence of permissions error (sometimes app.armor causes problems like this) but didn’t see evidence of that. I did an strace of the command and it doesn’t appear to be creating the file. Best Regards
ubuntu@ip-172-31-51-10:~$ cd qiime2-moving-pictures-tutorial/
ubuntu@ip-172-31-51-10:~/qiime2-moving-pictures-tutorial$ ls
demux-qual-plots.qzv demux.qza out raw-sequences raw-sequences.qza rep-seqs.qza Rplots.pdf sample-metadata.tsv table.qza table.qzv
ubuntu@ip-172-31-51-10:~/qiime2-moving-pictures-tutorial$ source activate qiime2
(qiime2) ubuntu@ip-172-31-51-10:~/qiime2-moving-pictures-tutorial$ qiime tools view demux-qual-plots.qzv
Viewing visualization failed while attempting to open /tmp/qiime2-archive-0zhj0c9b/9f5482db-77c1-4751-be22-1a8687e0fd82/data/index.html
(qiime2) ubuntu@ip-172-31-51-10:~/qiime2-moving-pictures-tutorial$
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
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!
Thanks for the rapid response. I just added the desktop package and everything was fine after that. Specifically I was able to successfully view the artifact. I’m evaluating scenarios for myself and others in my group and since we have a mixture of OSX and Windows (with X Server software) we might do work that way since we can create and AMI and spin up a large (or smaller) server when needed. Thanks again - I’m now working through the Qiime 2 Studio and have run into some problem though before I post that experience I’ll work through it some more to make sure I’ve done what was requested in the document. Best, Steve