Public bug reported:
This is a packaging issue; the igv shell script classpath is missing
/usr/share/java/commons-io.jar
The result is that when trying to create a .genome file from a fasta,
igv crashes with the following error:
INFO [2016-07-12 14:20:48,781] [CommandListener.java:106] [Thread-6]
Listening on port 60151
ERROR [2016-07-12 14:21:22,493] [DefaultExceptionHandler.java:49]
[AWT-EventQueue-0] Unhandled exception
java.lang.NoClassDefFoundError: org/apache/commons/io/FilenameUtils
at org.broad.igv.util.FileUtils.getRelativePath(FileUtils.java:118)
at org.broad.igv.util.FileUtils.getRelativePath(FileUtils.java:196)
at
org.broad.igv.feature.genome.GenomeImporter.createGenomeArchive(GenomeImporter.java:146)
at
org.broad.igv.feature.genome.GenomeManager.defineGenome(GenomeManager.java:1240)
at org.broad.igv.ui.IGV.doDefineGenome(IGV.java:508)
at org.broad.igv.ui.IGVMenuBar$13.actionPerformed(IGVMenuBar.java:585)
I have verified that adding the missing class lib to the shell script
fixes the problem.
ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: igv 2.3.68+dfsg-1
ProcVersionSignature: Ubuntu 4.4.0-28.47-generic 4.4.13
Uname: Linux 4.4.0-28-generic x86_64
NonfreeKernelModules: nvidia_uvm nvidia_modeset nvidia
ApportVersion: 2.20.1-0ubuntu2.1
Architecture: amd64
CurrentDesktop: XFCE
Date: Tue Jul 12 15:02:16 2016
InstallationDate: Installed on 2015-09-29 (287 days ago)
InstallationMedia: Xubuntu 15.04 "Vivid Vervet" - Release amd64 (20150422.1)
PackageArchitecture: all
SourcePackage: igv
UpgradeStatus: Upgraded to xenial on 2016-05-26 (46 days ago)
** Affects: igv (Ubuntu)
Importance: Undecided
Status: New
** Tags: amd64 apport-bug xenial
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https://bugs.launchpad.net/bugs/1602389
Title:
igv shell wrapper missing class dependency
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