Could not open IGV 2.2 in my mac osx 10.6.8

[haile...@gmail.com]

Hi,

I could not open IGV 2.2 today, but it worked fine before.

I got the following error. Thanks,

Hailei

<?xml version="1.0" encoding="utf-8"?>

<jnlp

  spec="6.0+"

  codebase="http://www.broadinstitute.org/igv/projects/current"

  href="igv_mm.jnlp">

  <information>

    <title>IGV 2.2</title>

    <vendor>The Broad Institute</vendor>

    <homepage href="http://www.broadinstitute.org/igv"/>

    <description>IGV Software</description>

    <description kind="short">IGV</description>

    <icon href="IGV_64.gif"/>

    <icon kind="splash" href="IGV_64.gif"/>

    <offline-allowed/>

<shortcut online="true">

 <desktop/>

 <menu submenu="IGV"/>

</shortcut>

  </information>

  <security>

      <all-permissions/>

  </security>

  <update check="always" policy="always"/>

  <resources>

    <java version="1.6+"

          initial-heap-size="256m" 

          max-heap-size="1100m" />

    <jar href="igv.jar" download="eager" main="true"/>

    <jar href="batik-codec.jar" download="eager"/>

    <jar href="goby-io-igv.jar" download="lazy"/>   

    <property name="java.net.preferIPv4Stack" value="true"/> 

    <property name="apple.laf.useScreenMenuBar" value="true"/>

    <property name="com.apple.mrj.application.growbox.intrudes" value="false"/>

    <property name="com.apple.mrj.application.live-resize" value="true"/>

    <property name="com.apple.macos.smallTabs" value="true"/>

    <property name="http.agent" value="IGV 2.2"/>

  </resources>

  <application-desc main-class="org.broad.igv.ui.Main"/>

</jnlp>

[Jacob Silterra]

That's not an error, that's the jnlp file which opens IGV. You need to open this with java web start. You can also download igv and run it locally

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Jacob Silterra
Software Engineer
Broad Institute

[andrea...@googlemail.com]

I ran into a similar problem - I was using IGV2.2 till about midnight, and then it stopped working. If I tried to launch it again from the icon on my desktop it gaves me the error message 'unable to launch IGV'. I deleted those files (in the Java preferences) and tried to launch it from the web, but that only downloads a igv.jnlp file and does nothing else. I would appreciate any help in how I can get IGV running again on my computer (Mac, 10.6.8).

Thanks,

Andi

[Steve Lianoglou]

Hi,

On Fri, Feb 1, 2013 at 12:15 PM, <andrea...@googlemail.com> wrote:
> I ran into a similar problem - I was using IGV2.2 till about midnight, and
> then it stopped working. If I tried to launch it again from the icon on my
> desktop it gaves me the error message 'unable to launch IGV'. I deleted
> those files (in the Java preferences) and tried to launch it from the web,
> but that only downloads a igv.jnlp file and does nothing else. I would
> appreciate any help in how I can get IGV running again on my computer (Mac,
> 10.6.8).

Download the binary distribution:

http://www.broadinstitute.org/igv/projects/downloads/IGV_2.2.5.zip

Unzip it
double-click the igv.command file in the unzipped folder

If there is an error that pops up, please let us know (verbatim) what that is.

HTH,
-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

[haile...@gmail.com]

The command line  "java -Xmx750m -jar igv.jar" works fine for me finally. 

Hailei

[David Heiman]

I'm having the exact same issue - just began today.

The More Information window has the error:

Which makes no sense, as all of our machines have 1.6+ of the JRE, and nothing about it has changed since yesterday.

The Launch File tab in the More Information window has the jnlp code that Hailei posted, and the Exception tab has the following:

JNLPException[category: System Configuration : Exception: null : LaunchDesc: 
<jnlp spec="6.0+" codebase="http://www.broadinstitute.org/igv/projects/current/" href="http://www.broadinstitute.org/igv/projects/current/igv_lm.jnlp">

  <information>
    <title>IGV 2.2</title>
    <vendor>The Broad Institute</vendor>
    <homepage href="http://www.broadinstitute.org/igv"/>
    <description>IGV Software</description>
    <description kind="short">IGV</description>

    <icon href="http://www.broadinstitute.org/igv/projects/current/IGV_64.gif" kind="default"/>
    <icon href="http://www.broadinstitute.org/igv/projects/current/IGV_64.gif" kind="splash"/>

    <shortcut online="true">
      <desktop/>
      <menu submenu="IGV"/>
    </shortcut>

    <offline-allowed/>

  </information>
  <security>
    <all-permissions/>
  </security>
  <update check="always" policy="always"/>
  <resources>

    <java initial-heap-size="268435456" max-heap-size="1887436800" version="1.6+"/>
    <jar href="http://www.broadinstitute.org/igv/projects/current/igv.jar" download="eager" main="true"/>
    <jar href="http://www.broadinstitute.org/igv/projects/current/batik-codec.jar" download="eager" main="false"/>
    <jar href="http://www.broadinstitute.org/igv/projects/current/goby-io-igv.jar" download="lazy" main="false"/>

    <property name="java.net.preferIPv4Stack" value="true"/>
    <property name="apple.laf.useScreenMenuBar" value="true"/>
    <property name="com.apple.mrj.application.growbox.intrudes" value="false"/>
    <property name="com.apple.mrj.application.live-resize" value="true"/>
    <property name="com.apple.macos.smallTabs" value="true"/>

  </resources>
  <application-desc main-class="org.broad.igv.ui.Main"/>

</jnlp> ]
at com.sun.javaws.Launcher.prepareLaunchFile(Launcher.java:797)
at com.sun.javaws.Launcher.prepareAllResources(Launcher.java:597)
at com.sun.javaws.Launcher.prepareToLaunch(Launcher.java:336)
at com.sun.javaws.Launcher.prepareToLaunch(Launcher.java:208)
at com.sun.javaws.Launcher.launch(Launcher.java:125)
at com.sun.javaws.Main.launchApp(Main.java:451)
at com.sun.javaws.Main.continueInSecureThread(Main.java:283)
at com.sun.javaws.Main$1.run(Main.java:116)
at java.lang.Thread.run(Thread.java:680)

Was http://www.broadinstitute.org/igv/projects/current/igv_lm.jnlp updated yesterday?  That might explain why Java Web Start has stopped working, and the binary can still be run directly.

Thanks,

David Heiman

Broad Institute of MIT and Harvard

 
On Thursday, January 31, 2013 4:45:49 PM UTC-5, Jacob Silterra wrote:

[David Heiman]

Could this: http://www.usatoday.com/story/tech/2013/01/31/apple-blocks-java-on-macs-due-to-vulnerabilities/1880783/

be the culprit?

[Jacob Silterra]

The JNLP hasn't been updated recently. Apples update is the most likely culprit, thanks for bringing this to our attention.

This vulnerability only affects java web start, one should still be able to download and run IGV locally.

-Jacob

[Craig Berry]

Yeah, I think there's something about Java 7 latest update that silently removes Java 6:

http://www.jnbridge.com/jn/blog/2013/01/28/java-7-update-silently-deletes-java-6-breaks-applications/