Issue loading IGV 2.4 on Windows 10

gabbs414 commented 7 years ago

Hi, I have downloaded the Java version 8 as well as the IGV browser for binary distribution. I tried to open the igv.bat file for Windows (I am running Windows 10) and I got the following message in my command window:

C:\WINDOWS\system32>for %x in ("C:\Users\gabbs\igv\IGV_2.4.1\igv.bat") do set BatchPath=%~dpsx

C:\WINDOWS\system32>set BatchPath=C:\Users\gabbs\igv\IGV_24~1.1\

C:\WINDOWS\system32>for %x in (C:\Users\gabbs\igv\IGV_24~1.1) do set BatchPath=%~dpsx

C:\WINDOWS\system32>set BatchPath=C:\Users\gabbs\igv\IGV_24~1.1\

C:\WINDOWS\system32>java -Xmx1200m -Dproduction=true -Djava.net.preferIPv4Stack=true -Dsun.java2d.noddraw=true -jar C:\Users\gabbs\igv\IGV_24~1.1\igv.jar WARN [2017-09-28 21:28:45,544] [Globals.java:138] [AWT-EventQueue-0] Development mode is enabled INFO [2017-09-28 21:28:45,569] [DirectoryManager.java:76] [AWT-EventQueue-0] Fetching user directory... INFO [2017-09-28 21:28:45,569] [DirectoryManager.java:76] Fetching user directory... INFO [2017-09-28 21:28:45,629] [DirectoryManager.java:171] [AWT-EventQueue-0] IGV Directory: C:\Users\gabbs\igv INFO [2017-09-28 21:28:45,629] [DirectoryManager.java:171] IGV Directory: C:\Users\gabbs\igv INFO [2017-09-28 21:28:45,634] [Main.java:154] [AWT-EventQueue-0] Startup IGV Version 2.4.1 09/25/2017 11:46 AM INFO [2017-09-28 21:28:45,634] [Main.java:155] [AWT-EventQueue-0] Java 1.8.0_144 INFO [2017-09-28 21:28:45,634] [Main.java:156] [AWT-EventQueue-0] Default User Directory: C:\Users\gabbs\Documents INFO [2017-09-28 21:28:45,635] [Main.java:157] [AWT-EventQueue-0] OS: Windows 10

INFO [2017-09-28 21:29:03,634] [GenomeManager.java:190] [pool-3-thread-1] Loading genome: http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome INFO [2017-09-28 21:29:05,039] [CommandListener.java:120] [Thread-7] Listening on port 60151

The main problem is that when IGV loads, hg19 is listed as the genome, but there are no genes in the bottom row and the drop-down menu for chromosomes is blank. Any ideas?

jrobinso commented 7 years ago

When IGV started did you get any dialogs wrt the windows firewall, and if so did you grant permissions?

Try shutting down IGV, then downloading the genome manually from http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg19.genome and saving it in the c:\Users\gabbs\igv\genomes folder, replacing the current copy if it exists

jrobinso commented 7 years ago

Also, particularly if you had earlier versions of IGV, try shutting down and renaming your "prefs.properties" file (e.g. to prefs.bak) and restart. If that solves the problem attaching your old prefs.properties file would be helpful for diagnosis.

helgathorv commented 7 years ago

We've managed to reproduce this problem. Until we can release a fix, try the following workaround:

go into the folder /igv/genomes
You'll see the genome files are named .genome.download, e.g. hg19.genome.download
Rename the file and remove the ".download" suffix, so that the name is .genome
restart IGV (or if you have multiple genomes in the dropdown menu you can just re-select the genome)

helgathorv commented 7 years ago

A fix was released today with IGV 2.4.2.

igvteam / igv

Issue loading IGV 2.4 on Windows 10 #467