The igv is now available via Ubuntu's repository, however, it won't run on the default Java RE (OpenJDK 11) or Oracle Java 12 available via PPA. Neither will a jar archive downloaded from the website. Below is the error message:

ERROR [2019-06-27 23:02:00,827] [DefaultExceptionHandler.java:49] [AWT-EventQueue-0] Unhandled exception
java.lang.NoClassDefFoundError: org/apache/commons/io/output/StringBuilderWriter
at org.broad.igv.util.HttpUtils.isRemoteURL(HttpUtils.java:120)
at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:109)
at org.broad.igv.util.ParsingUtils.openInputStream(ParsingUtils.java:96)
at org.broad.igv.util.ParsingUtils.openBufferedReader(ParsingUtils.java:78)
at org.broad.igv.prefs.PreferencesManager.load(PreferencesManager.java:168)
at org.broad.igv.prefs.PreferencesManager.loadUserPreferences(PreferencesManager.java:126)
at org.broad.igv.prefs.PreferencesManager.init(PreferencesManager.java:92)
at org.broad.igv.prefs.PreferencesManager.getPreferences(PreferencesManager.java:53)
at org.broad.igv.prefs.PreferencesManager.getPreferences(PreferencesManager.java:109)
at org.broad.igv.ui.Main.updateTooltipSettings(Main.java:175)
at org.broad.igv.ui.Main.initApplication(Main.java:162)
at org.broad.igv.ui.Main.access$000(Main.java:72)
at org.broad.igv.ui.Main$1.run(Main.java:102)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:389)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.io.output.StringBuilderWriter
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:583)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
... 26 more
INFO [2019-06-27 23:02:01,832] [ShutdownThread.java:47] [Thread-1] Shutting down

Reporter: Dzmitry Batrakou
E-mail: dzmitry.batrakou@path.ox.ac.uk