I have a newly installed and seemingly perfectly functioning qiime2 running on out new server with the latest Ubuntu.
I attempted to install q2studio as per QIIME 2 Studio (q2studio) — QIIME 2 2019.7.0 documentation.
At npm install && npm run build I got a warning:
npm WARN optional Skipping failed optional dependency /chokidar/fsevents:
npm WARN notsup Not compatible with your operating system or architecture: [email protected]
but the installation looked OK otherwise.
npm start gave me lots of error messages as shown below, starting with
MoTTY X11 proxy: Unsupported authorisation protocol
Failed at the [email protected] start script 'cross-env NODE_ENV=production electron -r babel-register build/main.js'.
I made sure that both npm and node.js are the most recent versions, so the npm suggests that "this is most likely a problem with the q2studio package, not with npm itself."
After checking the blogs here I also did "which pip" and "conda list".
I am attaching the outputs of the commands as well as the content of the
...q2studio-2019.7.0/npm-debug.log file in Win (txt, CR/LF) and linux(linux, LF) format
q2studio_install_problem.txt (34.3 KB)
q2studio_install_problem.linux.txt (33.8 KB)
Welcome to the forum, and thanks for the log files, those are super helpful!
It looks like there’s an issue with the X11 forwarding in your SSH connection. How are you connecting to the server, and do you have a local X11-server to receive the commands from the remote server?
Given that newer distros are starting to move to wayland, there may also be some other issues here, since wayland does not to my knowledge replace the ability to transfer graphics over a network like X11 does.
Thanks a lot for looking at my problem.
I am sitting in front of a Win computer, using Mobaxterm. It works perfectly for all other graphic applications, like Xterm, Firefox (incl. qiime tools view), etc…
However, it may not work if I sudo su to the root, because that is just a login-like thing and not graphical.
Since I was afraid the there was some authorization issue used sudo a lot of time, and that might have caused the problem.
However, now I just logged in, activated qiime2-2019.7 and typed npm start, which again resulted in the same error messages, although xterm opened a window.
I do not know. … I am confused a bit. (Plus slightly panicking.)
I also have a dada2-R problem that needs investigated before I can report it here, but this is a brand new very modern server and it should be perfect, so I do not really suspect H/W malfunctions.
If you have any further suggestions I would be more than happy to try whatever to get this whole q2 suite running. After preliminary trials and tests I designed a rather large project with qiime in mind that seem to start with some obstacles.
No need to worry! It sounds like everything is working as it should be, it’s just q2studio who is the odd-one-out. This is not unusual, it’s a very very alpha-release kind of interface. Since it sounds like you have big plans, I would recommend not actually using q2studio, the UI isn’t quite there yet, and this is unlikely to be the first issue you run into.
Instead I would recommend using the more battle-tested interfaces like
q2cli or the
Artifact API (if you know Python). Both are great, and shouldn’t cause any issues.
I agree, I would expect your hardware is just fine. If you’d like, please open another topic about the DADA2 situation and we can help debug!