Load from server and genome initialization

[Toffee]

Hello,

I've recently started using IGV v2.0.9 from v1.5 from behind a
corporate firewall. Although I was able to access the genomes and
Broad server without any problems (without specifying the proxy) when
using v1.5, when using v2.0.9 I am now unable to. Upon loading IGV I
get an error message saying IGV could not connect to the genome
server.
I've tried the workaround ("Proxy") discussed on the FAQ but have been
unable to get v2.0.9 to work the same way that v1.5 does. Can anyone
help please?

Thanks,
Rob

[James Robinson]

Hi,

The workaround shouldn't be neccessary,  that is for a first-time install,  however you might need to enter your proxy information in the preferences tab.   Have you tried that?  I realize you didn't for 1.5, but currently its neccessary for 2.0 at some sites.  For those who are interested in the details we switched from the "plain" JDK url classes to Apache HttpClient and this has necessitated explicit proxy information.  I'm investigating why and if anything can be done about it,  short of rolling back to the JDK classes.

You get to the proxy information from View > Preferences > Proxy tab.  If you've entered that already and are still having connection problems let us know.

-- Jim

[Michael]

hi,

i experienced this problem too. thanks for the suggested fix, setting
the proxy info in View > Preferences > Proxy tab.

that sort of worked. when i start v2.0, igv no longer hangs for
minutes, timing out, i imagine, but it still gives me an error that it
can't connect to the broad. not connecting is fine w/ me because we
use all local files. preventing the timeout is good, but i'm still a
bit curious on why it doesn't go through our proxy server.

fyi, i tried three different methods in the proxy tab, with the same
results for all. i checked the 'use authorization' box and supplied a
user name and password. i also tried checking the box, but not
supplying a user name and password, hoping i would be prompted with a
dialog box. i was never prompted w/ a dialog and neither method got me
through our firewall - both said they couldn't connect. i also tried
it without checking the 'use auth' box hoping i would be prompted, but
i never got the prompt.

i'm not sure there's a question in there because mostly this anomaly
does not interfere with my work... just curious and thought you might
want to know since it sounds like you're employing a new method.

thanks
mike

On Sep 22, 11:51 am, James Robinson <jrobi...@broadinstitute.org>
wrote:

[Jim Robinson]

Hi Mike,

Thanks for the report.  There are a lot of proxy types and configurations out there, apparently, and we do not have the resources to mirror them all hear for tests.  Everything works fine with our linux / squid proxy.

I just checked in some changes that seems to have solved these problems for at least a couple of sites.  If you woudn't mind trying the "early access" IGV from your site and let us know if it fixes the problem that would be helpful.   You can get this version from our website here  http://www.broadinstitute.org/igv/projects/dev/,  or launch it directly from this link

http://www.broadinstitute.org/igv/projects/dev/igv_dev.jnlp

Here's a brief history of this problem for the curious.   In IGV 1.5 we used the JDK HttpURLConnection class to do connections and deal with proxies and life was good.  For 2.0 we switched to Apache HttpClient (4.1),  mostly to satisfy some requirements of another project integrating with IGV.   Since then we have had several reports of the form  "IGV 1.5 worked with my proxy but IGV 2.0 does not".   After much googling and reading docs and trying many tests with the help of a user  I have thrown in the towel and reverted back to HttpURLConnection.   


-- Jim

[Toffee]

Hi Jim,

just started trying v2.0.10 and, as far as I can tell so far, the
proxy issue seems to have been resolved for me - thanks!

Rob