Starting IGV under Windows doesn't work

[Boyke Bunk]

Hello!

I tried to start IGV 2.2.5 under Windows 7, 64bit with igv.bat and got following error. Whats going wrong?

Thx,
Boyke

C:\IGV_2.2.5>java  -Xmx1200m -Djava.net.preferIPv4Stack=true -Dsun.java2d.noddra
w=true -jar C:\IGV_22~1.5\\igv.jar
Fetching user directory... INFO [2013-01-30 15:11:10,910]  [DirectoryManager.jav
a:149] [main]  IGV Directory: C:\Users\bob10\igv
INFO [2013-01-30 15:11:10,918]  [Main.java:72] [main]  Startup  IGV Version 2.2.
5 (7)01/25/2013 02:05 PM
INFO [2013-01-30 15:11:10,919]  [Main.java:73] [main]  Java 1.7.0_11
INFO [2013-01-30 15:11:10,920]  [Main.java:74] [main]  Default User Directory: C
:\Users\bob10\Documents
ERROR [2013-01-30 15:11:14,283]  [GenomeManager.java:673] [main]  Error fetching
 genome list:
java.net.SocketException: Connection reset
        at java.net.SocketInputStream.read(Unknown Source)
        at java.net.SocketInputStream.read(Unknown Source)
        at java.io.BufferedInputStream.fill(Unknown Source)
        at java.io.BufferedInputStream.read1(Unknown Source)
        at java.io.BufferedInputStream.read(Unknown Source)
        at sun.net.www.http.HttpClient.parseHTTPHeader(Unknown Source)
        at sun.net.www.http.HttpClient.parseHTTP(Unknown Source)
        at sun.net.www.http.HttpClient.parseHTTP(Unknown Source)
        at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown So
urce)
        at java.net.HttpURLConnection.getResponseCode(Unknown Source)
        at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:539)
        at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:481)
        at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:477)
        at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:185)

        at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:179)

        at org.broad.igv.feature.genome.GenomeManager.getServerGenomeArchiveList
(GenomeManager.java:630)
        at org.broad.igv.feature.genome.GenomeManager.getGenomeArchiveList(Genom
eManager.java:578)
        at org.broad.igv.feature.genome.GenomeManager.buildGenomeItemList(Genome
Manager.java:763)
        at org.broad.igv.ui.IGVCommandBar.initializeGenomeList(IGVCommandBar.jav
a:181)
        at org.broad.igv.ui.IGV$StartupRunnable.run(IGV.java:2204)
        at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:39)
        at org.broad.igv.ui.IGV.startUp(IGV.java:2164)
        at org.broad.igv.ui.Main.open(Main.java:159)
        at org.broad.igv.ui.Main.main(Main.java:66)
INFO [2013-01-30 15:11:15,968]  [GenomeManager.java:882] [main]  java.io.FileNot
FoundException: C:\Users\bob10\igv\genomes\user-defined-genomes.txt (Das System
kann die angegebene Datei nicht finden)
ERROR [2013-01-30 15:11:15,972]  [DefaultExceptionHandler.java:42] [main]  Unhan
dled exception
java.lang.ArrayIndexOutOfBoundsException: 0
        at org.broad.igv.ui.IGVCommandBar.getModelForGenomeListComboBox(IGVComma
ndBar.java:556)
        at org.broad.igv.ui.IGVCommandBar.refreshGenomeListComboBox(IGVCommandBa
r.java:543)
        at org.broad.igv.ui.IGVCommandBar.initializeGenomeList(IGVCommandBar.jav
a:182)
        at org.broad.igv.ui.IGV$StartupRunnable.run(IGV.java:2204)
        at org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:39)
        at org.broad.igv.ui.IGV.startUp(IGV.java:2164)
        at org.broad.igv.ui.Main.open(Main.java:159)
        at org.broad.igv.ui.Main.main(Main.java:66)

[Jacob Silterra]

That looks like a problem with your internet connection being unable to download the genome archive list. Are you behind any kind of firewall or proxy?

-Jacob

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Jacob Silterra
Software Engineer
Broad Institute

[Boyke Bunk]

Behind a proxy. But I am unable to access Proxy settings within IGV as I am not able to start it. Furthermore it should start even without genomes, or?

Boyke

[Jacob Silterra]

IGV isn't designed to run well without a genome loaded, although you're right that you should at least be able to open it. The latest snapshot build should have this fixed: https://www.broadinstitute.org/software/igv/download_snapshot

You can also load a genome from a local file using the -g option, see https://www.broadinstitute.org/software/igv/startingIGV.

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[Boyke Bunk]

The snapshot works fine for me!

Boyke