Whilst the current release versions (2.11.1.*) of the Jalview installers run with a bundled Java 1.8 runtime environment, Jalview development is using Java 11 (a much more recent LTS version of Java), but is maintaining support for Java 1.8 especially for the current release versions.
"We were unable to download the necessary files after five attempts. You can try running the application again, but if it fails you may need to uninstall and reinstall."
(like this screenshot:
Jalview uses a launcher (called getdown, see https://github.com/threerings/getdown) that runs an auto-updater for Jalview and verifies Jalview files by checking the Jalview web site. Whilst the launcher checks for existing system proxy settings, sometimes it does not find those settings. In this case it may pop up a window asking for proxy settings. If this does not happen, and proxy settings are required, you can create a file called
Problems on Windows:
If your installation of Jalview goes fine, but double clicking on the Jalview icon does not produce any error message, window or any other activity (other than the spinning blue circle) this might be caused by a space character in Jalview's installation folder. To fix this:
When Jalview is run on WIndows machines with high resolution displays (e.g. 4K, retina, etc) resolution screens, you might find that all the menus, window titles, and alignment data are really tiny. That's because on high-resolution displays, all the windows and fonts have to be magnified so that you can read them, and the fix is to ask Windows to do the same for the Jalview application.
Instructions on how to do this can be found in several places on the 'net. Your milage may vary so please let us know if you are having problems via the jalview-discuss AT jalview.org mailing list !
See https://pivotce.com/2017/12/11/fix-java-applications-for-high-dpi-display/ for the following solution which should work for launching Jalview via webstart on machines with Java 8 installed.
- Close Jalview
- Find java.exe and/or javaw.exe likely found in C:\Program Files\Java\jre(version#)\bin.
- Right click on it and select -> Properties
- Go to Compatibility tab
- Check Override high DPI scaling behavior.
- Choose System for Scaling performed by:
- Click OK
- Relaunch Jalview
1. Save your work and shut down Jalview
2. Open a Terminal window (use spotlight or the Launcher and type 'Terminal' to locate the Terminal App), and type:
defaults write -g CGFontRenderingFontSmoothingDisabled -bool NO
3. Start Jalview again and load an alignment to check that the fonts are now legible.
If you are running Jalview 2.10.0 under Ubuntu or some other (possibly GTK based) Linux desktop, you may find that after opening the Sequence Fetcher, you are presented with a dialog box just showing 'OK' and 'Cancel' buttons, but nothing much else. The empty panel is due to an underlying problem with Java, but you can still choose from the list of databases with the keyboard !