Uninstall igv 2.0 from ubuntu

[juhan]

I just tried to install igv 2.0 on ubuntu and had trouble importing
genome file.
Someone told me there is a bug on the recent version, so I tried to
uninstall 2.0.
I simply deleted IGV 2.0 icon from the desktop and looked several
folders in vain.
As 2.0 version worked fine on Mac, I tried to restart 2.0 by clicking
downloading from IGV website,
and it would not start again.
How can I completely uninstall the previous 2.0 version on ubuntu?
I want to try 1.5 on ubuntu system.
-juhan

[juhan]

# just additional information about my trouble (ubuntu 11)
igv_hm.jnlp for 2.0 version would not start anything.
igv_hm.jnlp for 1.5 version would produce error message as follows;
-----
Fatal: Read Error: Could not read or parse the JNLP file.
net.sourceforge.jnlp.LaunchException: Fatal: Read Error: Could not
read or parse the JNLP file.
at net.sourceforge.jnlp.Launcher.fromUrl(Launcher.java:491)
at net.sourceforge.jnlp.Launcher.launch(Launcher.java:283)
at net.sourceforge.jnlp.runtime.Boot.run(Boot.java:199)
at net.sourceforge.jnlp.runtime.Boot.run(Boot.java:51)
at java.security.AccessController.doPrivileged(Native Method)
at net.sourceforge.jnlp.runtime.Boot.main(Boot.java:165)
Caused by: net.sourceforge.jnlp.ParseException: Invalid value for heap
size (10g)
at net.sourceforge.jnlp.JREDesc.checkHeapSize(JREDesc.java:143)
at net.sourceforge.jnlp.JREDesc.<init>(JREDesc.java:68)
at net.sourceforge.jnlp.Parser.getJRE(Parser.java:323)
at net.sourceforge.jnlp.Parser.getResourcesDesc(Parser.java:267)
at net.sourceforge.jnlp.Parser.getResources(Parser.java:230)
at net.sourceforge.jnlp.JNLPFile.parse(JNLPFile.java:591)
at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:178)
at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:162)
at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:148)
at net.sourceforge.jnlp.Launcher.fromUrl(Launcher.java:477)
... 5 more
Caused by:
net.sourceforge.jnlp.ParseException: Invalid value for heap size (10g)
at net.sourceforge.jnlp.JREDesc.checkHeapSize(JREDesc.java:143)
at net.sourceforge.jnlp.JREDesc.<init>(JREDesc.java:68)
at net.sourceforge.jnlp.Parser.getJRE(Parser.java:323)
at net.sourceforge.jnlp.Parser.getResourcesDesc(Parser.java:267)
at net.sourceforge.jnlp.Parser.getResources(Parser.java:230)
at net.sourceforge.jnlp.JNLPFile.parse(JNLPFile.java:591)
at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:178)
at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:162)
at net.sourceforge.jnlp.JNLPFile.<init>(JNLPFile.java:148)
at net.sourceforge.jnlp.Launcher.fromUrl(Launcher.java:477)
at net.sourceforge.jnlp.Launcher.launch(Launcher.java:283)
at net.sourceforge.jnlp.runtime.Boot.run(Boot.java:199)
at net.sourceforge.jnlp.runtime.Boot.run(Boot.java:51)
at java.security.AccessController.doPrivileged(Native Method)
at net.sourceforge.jnlp.runtime.Boot.main(Boot.java:165)

[James Robinson]

Hi,

The startup error below indicates you are trying to launch with the 10 GB option which is more than your Java virtual machine can do.  Try launching with the lowest memory option and then increase it (left to right as the buttons are arranged) until it fails.   You can only use the large memory option if you are running a 64-bit java and have the memory available.

Jim

[James Robinson]

Hi, 

You do not need to completely uninstall to try version 1.5,  they are independent.  You can have both on your machine at the same time.  The symptom you describe is lilkely caused by a failure to connect to our genome server, which in turn could be caused by proxy settings.  Are you behind a firewall or proxy?  Have you tried setting the proxy settings in the user preferences window (View > Preferences > Proxy tab).

Again,  you should not need to "completely uninstall",  if you do wish to do that you need to flush your java cache.   The procedure for doing this is platform specific, but you can use the "javaws" application to do it on most platform/JDK combinations.  This app can be launched from the command line as follows

javaws -viewer

Please continue to report bugs here, its the only way they get fixed :).

Jim

[juhan]

Hi,

I'm running igv on 16GB memory with i7 processor with 64 bit Java.
I0 GB mode ran first, but I could not start it again, after I deleted
the icon from the desktop on ubuntu.
I can not restore the deleted file too. When I restored it, it came as
***.desktop and did not do anything when I double-clicked it.

Juhan

[James Robinson]

Hi,

The error message in the log is from the JDK, even before IGV starts, indicating that it could not start with the memory requested.   This is an Ubuntu/Java environment question.    However,  starting with more than 2GB should never be necessary,  if you feel you need more than that perhaps we can discuss other solutions, such as using the binary indexed formats available.

I'm not familiar enough with the Ubuntu desktop to help with that.   However if you want complete control you can download  the "binary distribution", which is a zip file.  Just unzip it and follow the instructions in "readme" for launching.   This is completely self-contained and does not depend on your java web start environment.

-- Jim

[juhan]

Hi Jim,

Thanks for the advice.

[1]
I downloaded 1.5 and its running now.
But, when I loaded Bam file I could not see short read alignments,
except 'zoom in to see...' message.
When I used same files (genome, Bam and others) on Mac it worked
beautifully though.
Any idea?

[2]
In my trials, 2.0 has trouble loading genome on Ubuntu no matter what
platform I used.
After loading genome there is a window suspended saying "loading
genome"
I would use 1.5 binary distribution for now, but I hope this would be
fixed
for Ubuntu users sooner or later.

Thanks.

Juhan

On Aug 9, 6:30 pm, James Robinson <jrobi...@broadinstitute.org> wrote:
> Hi,
>

[James Robinson]

Hi,

You need to zoom in until you don't see the "zoom in to see" message,
which is < 30kb by default have you done that?

I don't think there is a general Linux problem, we have too many
linux users for that to be the case (thousands of linux launches
weekly). Its more likely network related, particularly if you are
behind a proxy. The network client changed for 2.0, from the plain
JDK classes to Apache HttpClient. Some users have had problems with
proxies after this change, but in most cases we've been able to work
it out. The only open issue with this I'm aware of is with an IIS
proxy doing NTLM authentication.

Are you behind a proxy? Also, could you send the igv.log file from
the Ubuntu box to igv-...@broadinstitute.org. Its possible I will
be able to resolve the error that way.

Jim

[juhan]

Hi,

I'm now successfully running 1.5.64 binary distribution on Ubuntu.

Binary distribution of 2.0 shows "genome loading" window forever,
when I tried to import fasta genome sequence file.
Other than that it seems fine, but I decided to stick to 1.5.64 for
now.
Someone that I know also told me she had trouble loading genome
with 2.0 igv on linux so they are using older version.

Anyway, it's running now ! :)
I still cannot start igv directly from the web after I deleted the igv
icon
from the desktop (weird). But, I will look into that later since I
have a running
version now.

Thank you so much for helps.

Juhan



On Aug 10, 11:21 am, James Robinson <jrobi...@broadinstitute.org>
wrote:
> Hi,
>

> You need to zoom in until you don't see the "zoom in to see" message,
> which is < 30kb by default have you done that?
>
> I don't think there is a general Linux problem,  we have too many
> linux users for that to be the case (thousands of linux launches
> weekly).   Its more likely network related,  particularly if you are
> behind a proxy.   The network client changed for 2.0,  from the plain
> JDK classes to Apache HttpClient.   Some users have had problems with
> proxies after this change, but in most cases we've been able to work
> it out.   The only open issue with this I'm aware of is with an IIS
> proxy doing NTLM authentication.
>
> Are you behind a proxy?  Also,  could you send the igv.log file from

> the Ubuntu box to igv-h...@broadinstitute.org.   Its possible I will

[juhan]

This is just a followup for the installation issue with 2.0 version.

After I installed Sun Java (replacing Java installed in default in
Ubuntu),
it seems all the issues gone.

Juhan

[James Robinson]

Thanks very much for letting us know.

Jim