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  1. User Support
  2. HELP-322

Impossible to get running on Ubuntu 18.04.02

          Details

            Description

            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

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                support Support (Inactive) created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Resolution Done [ 10000 ]
                Status Open [ 1 ] Closed [ 6 ]
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                ann.loraine Ann Loraine added a comment -

                Replied:

                Hello,

                It looks like you were trying to get in touch with someone at the IGV project but found the IGB site instead?

                IGB is a different genome browser, developed several years before IGV. I'm not sure why, but the Broad developers decided to use a very similar name, and it's been causing a lot of confusion ever since.

                IGB Web site is https://bioviz.org

                Source code repository:
                IGB - https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/
                Warm regards,

                Ann

                Show
                ann.loraine Ann Loraine added a comment - Replied: Hello, It looks like you were trying to get in touch with someone at the IGV project but found the IGB site instead? IGB is a different genome browser, developed several years before IGV. I'm not sure why, but the Broad developers decided to use a very similar name, and it's been causing a lot of confusion ever since. IGB Web site is https://bioviz.org Source code repository: IGB - https://bitbucket.org/lorainelab/integrated-genome-browser/src/master/ Warm regards, Ann
                ann.loraine Ann Loraine made changes -
                Status Closed [ 6 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18583 ] Fall 2019 Workflow Update [ 20706 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 20706 ] Revised Fall 2019 Workflow Update [ 22915 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    support Support (Inactive)
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                    • Created:
                      Updated:
                      Resolved: