Assistance with Proxy Settings

[Dario Strbenac]

Hello,

I've been able to get Dropbox working on my university network, and was hoping I could use the same proxy settings for IGV 2.1. I've entered the same settings, but it cannot connect to the genome server. Can anyone tell me what to enter next ?

- Dario.

[Jim Robinson]

Dario,

That should do it.  Has it worked in the past?  Perhaps putting the full name of the server would help (siv.whatever.com).   If you are still experiencing this problem please send us your igv.log file  (to igv-...@broadinstitute.org) and we'll work from there.

Jim

[Chee-Hong Wong]

Jim: Does IGV handle SOCKS5 proxy?

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[James Robinson]

Ahh, that's probably the problem.  Thanks.   I had thought the JDK classes we used would handle that, and they should, but not in the way I am using them.    I will need to make some coding changes to fix this.

Dario,  in the meantime you could probably fix this by downloading the zip version and setting the properties on the command line,  as outlined below (from http://docs.oracle.com/javase/6/docs/technotes/guides/net/proxies.html).   Basically you would edit the shell script or just start from the command line with something like this

java -DsocksProxyHost=siv.whatever.edu -Xmx2000m  igv.jar

Also,  you might need to edit your prefs.properties file and delete the proxy related entries there, or just delete the whole file.

If you are able to try this let us know the result.     I will create a test version for you to try via Java web start,  hopefully later today.

Jim 

2.4) SOCKS

The SOCKS protocol, as defined in RFC 1928, provides a framework for client server applications to safely traverse a firewall both at the TCP and UDP level. In that sense it is a lot more generic than higher level proxies (like HTTP or FTP specific proxies). J2SE 5.0 provides SOCKS support for client TCP sockets.

There are 2 system properties related to SOCKS:

• socksProxyHost for the host name of the SOCKS proxy server
• socksProxyPort for the port number, the default value being 1080

Note that there is no dot ('.') after the prefix this time. This is for historical reasons and to ensure backward compatibility. Once a SOCKS proxy is specified in this manner, all TCP connections will be attempted through the proxy.

Example:

$ java -DsocksProxyHost=socks.mydomain.com GetURL

Here, during the execution of the code, every outgoing TCP socket will go through the SOCKS proxy server at socks.mydomain.com:1080.

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[Jim Robinson]

Dario,  

When you get a chance could you try the "early access" IGV?  It now has a pulldown to specify the proxy type,  you will want to choose "SOCKS".   Theoretically this should work with SOCKS v4 or v5,  I have no way to test it myself at the moment.   Please let us know the result.  

Thanks

Jim

[Dario Strbenac]

It is successful in loading the genomes list.

[Dario Strbenac]

It's not working anymore.

I get :

ERROR [2012-09-12 10:35:18,360]  [LoadFromServerAction.java:106] [AWT-EventQueue-0]  Error loading genome registry file
java.net.SocketException: Malformed reply from SOCKS server

I'm not sure what changed since I used it before. Does anyone else use such a proxy server ? Can you tell about your experience ?

[Dario Strbenac]

Please disregard. I got myself confused about which port the server uses. It's OK now.

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