"Malformed reply from SOCKS server while loading session file " with SOCKs proxy configured

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Malcolm Cook

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May 21, 2016, 2:11:09 PM5/21/16

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Hi,

I have used SSH to configure socks proxy from home to work network.

ssh -N -f -C -D 1080 workbox.domain.org

It works. I can browse intranet behind our firewall if I launch chrome as:

google-chrome --proxy-server="socks://localhost:1080" &

Alas, configuring IGV similarly, using "view > preferences > proxy >

[x] Use proxy

Proxy host: localhost

Proxy port: 1080

Proxy type: SOCKS

And when I try to " File > Load From URL" and provide the URL to a session which loads via URL fine behind the firewall, I get

"Malformed reply from SOCKS server"

Referring to https://groups.google.com/d/msg/igv-help/H-PjFXJZZds/qnUDqfF4Z5YJ suggests my configuration is as expected.

Researching suggests I might need to augment how I set up the proxy perhaps by adding "-o 'GatewayPorts yes' -g "

ssh -o 'GatewayPorts yes' -g -N -f -C -D 1080 workbox.domain.org

Alas, no dice, and I welcome any diagnostics or suggestions how to circumvent this (besides "go to work").

Thanks, and, full backtrace below,

~Malcolm

malcook@vishnu:~$ channel 26: open failed: connect failed: Connection refused

ERROR [2016-05-21 12:45:29,905] [IGV.java:1462] [pool-1-thread-10] Error loading session session : <br>  http://bioinfo/n/core/Bioinformatics/analysis/lmw/hox_in_lamprey/pmg1.d2/full.igv_session.xml<br>Malformed reply from SOCKS server

java.net.SocketException: Malformed reply from SOCKS server

at java.net.SocksSocketImpl.readSocksReply(SocksSocketImpl.java:130)

at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:502)

at java.net.Socket.connect(Socket.java:579)

at sun.net.NetworkClient.doConnect(NetworkClient.java:175)

at sun.net.www.http.HttpClient.openServer(HttpClient.java:432)

at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)

at sun.net.www.http.HttpClient.<init>(HttpClient.java:211)

at sun.net.www.http.HttpClient.New(HttpClient.java:308)

at sun.net.www.http.HttpClient.New(HttpClient.java:326)

at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:998)

at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:977)

at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:852)

at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1302)

at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:468)

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:713)

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:618)

at org.broad.igv.util.HttpUtils.openConnection(HttpUtils.java:614)

at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:220)

at org.broad.igv.util.HttpUtils.openConnectionStream(HttpUtils.java:214)

at org.broad.igv.util.ParsingUtils.openInputStreamGZ(ParsingUtils.java:111)

at org.broad.igv.ui.IGV.restoreSessionSynchronous(IGV.java:1420)

at org.broad.igv.ui.IGV$8.run(IGV.java:1397)

at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:72)

at java.util.concurrent.FutureTask.run(FutureTask.java:262)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

at java.lang.Thread.run(Thread.java:745)

INFO [2016-05-21 12:45:29,906] [MessageUtils.java:74] [pool-1-thread-10] <html>Unexpected error: java.net.SocketException: Malformed reply from SOCKS server.<br>See igv.log for more details

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