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aidenlab / Juicebox

Visualization and analysis software for Hi-C data -
https://aidenlab.org/juicebox
MIT License
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Juicebox Opens a Blank Window in Linux #863

Open taylorjtamu opened 5 years ago

taylorjtamu commented 5 years ago

When attempting to launch Juicebox on Scientific Linux 7.7 with OpenJDK JRE 64-Bit 1.8.0, regardless of the version of Juicebox attempted it opens a completely blank window. There is a titlebar and a space below that but nothing else is drawn at all. On old enough versions (1.8.8 specifically in this test), there is a popup window with a titlebar that states "Update Information" and has a clickable (but invisible) hyperlink in it. Nothing is drawn other than the titlebar and title.

This started after we had to do a system reinstall to update the operating system.

I highly suspect that we're simply missing some dependency that I'm not aware of and am mostly trying to figure out what that might be. Does Juicebox have logs stored anywhere that would point at the dependency I might be missing? Is there a listing anywhere I could compare against?

sa501428 commented 5 years ago

Are you using the jar? Have you tried running the GUI via command line? java -jar juicebox.jar

On Mon, Oct 28, 2019, 11:20 AM taylorjtamu notifications@github.com wrote:

When attempting to launch Juicebox on Scientific Linux 7.7 with OpenJDK JRE 64-Bit 1.8.0, regardless of the version of Juicebox attempted it opens a completely blank window. There is a titlebar and a space below that but nothing else is drawn at all. On old enough versions (1.8.8 specifically in this test), there is a popup window with a titlebar that states "Update Information" and has a clickable (but invisible) hyperlink in it. Nothing is drawn other than the titlebar and title.

This started after we had to do a system reinstall to update the operating system.

I highly suspect that we're simply missing some dependency that I'm not aware of and am mostly trying to figure out what that might be. Does Juicebox have logs stored anywhere that would point at the dependency I might be missing? Is there a listing anywhere I could compare against?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/aidenlab/Juicebox/issues/863?email_source=notifications&email_token=ABRT23MFJIPS4ZC6R3A2G7TQQ4GLZA5CNFSM4JF4VU7KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HU2AXLA, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABRT23OK2ANGHL6DGEAAIBDQQ4GLZANCNFSM4JF4VU7A .

taylorjtamu commented 5 years ago

Yes, sorry I didn't specify. This is using the jar:

java -jar Juicebox_1.11.08.jar java -jar Juicebox_1.8.8.jar etc

I just tested logging into the box directly (physically) and was able to get Juicebox to display properly. It seems to be an issue with trying to run it remotely over our XRDP setup. I tested with another Linux box remotely and had the same issue. I tested additionally with another system that's running Scientific Linux 6.10 over the XRDP/remote connection and Juicebox displayed the GUI properly.

Is this a known problem? Are there any configurations that I should modify to allow this to work? Are there any logs from Juicebox that might be helpful in resolving this? Unfortunately, our users only have remote access to these systems as they are rack mounted and kept in a secure server room.

sa501428 commented 5 years ago

Do you have an admin at your institution? @weiszd @nchernia any thoughts?

sa501428 commented 5 years ago

Also this may be a better discussion for our forum: aidenlab.org/forum.html

taylorjtamu commented 5 years ago

Yes, I have admin and am the main administrator for these systems. Ah, I wasn't aware of the forum. i can move this there if it's better.