X11/X-Windows

[kaps]

how do I use X11/X-Windows when running igv

[GenoMax]

Here is a guide on how to do this: http://www.no.embnet.org/guides/puttyandxming.pdf

[kaps]

Originally Posted by GenoMax

Here is a guide on how to do this: http://www.no.embnet.org/guides/puttyandxming.pdf

I am using MobaXterm on windows to access the server. Can it do the same thing as putty? If so then I need advise on how to explore instead of installing a new program!

Thanks

[GenoMax]

No installation is required for PuTTY (it is a very small program that you run directly). http://www.chiark.greenend.org.uk/~s.../download.html

You would want to use X11 only if a reliable (good, speed-wise) internet connection is available.

[kaps]

Originally Posted by GenoMax

No installation is required for PuTTY (it is a very small program that you run directly). http://www.chiark.greenend.org.uk/~s.../download.html

You would want to use X11 only if a reliable (good, speed-wise) internet connection is available.

For my case what will be the host name or IP address?

Thanks

[GenoMax]

Originally Posted by kaps

For my case what will be the host name or IP address?

Thanks

IP address or name of the server you are using.

[kaps]

Originally Posted by GenoMax

IP address or name of the server you are using.

This gives a blank configured session. is this normal?

[GenoMax]

Originally Posted by kaps

This gives a blank configured session. is this normal?

Are you using the "basic host name" you use with MobaXterm and the same user name with PuTTY?

MobaXterm appears to include some form of X11 so you may be able to use that program (http://mobaxterm.mobatek.net/documentation.html#2_3_5).

[kaps]

Originally Posted by GenoMax

Are you using the "basic host name" you use with MobaXterm and the same user name with PuTTY?

MobaXterm appears to include some form of X11 so you may be able to use that program (http://mobaxterm.mobatek.net/documentation.html#2_3_5).

I have succeeded in configuring putty, however when I launch Xming, I do not an X-shaped icon on the right corner of your Windows taskbar (bottom of the Screen) as stated in the manual and when I type, this happens:
yyyy$ xclock &
> [1] 4556
> [yyyy ~]$ Error: Can't open display:

what is the problem?\

[GenoMax]

Sounds like you were not able to install X-ming application correctly (or it is not running, check in your windows task manager).

What do you see when you type this command in terminal on server (remove the actual name of the server when posting output/replace with xxx)?

$ echo $DISPLAY

[kaps]

Nothing is seen

[GenoMax]

That means you were not able to configure PuTTY correctly. If you did do the "Enable X11 forwarding" on PuTTY you generally have to save the settings. Log out and log back in to the server to see the result of command above. Give that a try.

[kaps]

Its now set. I see the eyes and the clock (though the x shaped icon cannot be seen!).

Now that putty is working, How do i use it to run igv?

Thanks

[GenoMax]

Download IGV from Broad Institute and run it following the instructions: http://www.broadinstitute.org/igv/

[kaps]

Hello, If am running IGV on putty, will the required version be, Binary Distribution?

[GenoMax]

Correct. Don't use the webstart.

[kaps]

Noted. it seems the webstart options are for standalone, mac or windows OS?

Did you say that Putty does not need a strong internet compared to Mobaxterm?

[GenoMax]

Originally Posted by kaps

Did you say that Putty does not need a strong internet compared to Mobaxterm?

Reliability (and speed) of the internet connection is important when you are trying to use X11 over internet. That requirement is independent of specific terminal program you are planning to use (putty etc). You are going to get the best experience if use X11 while you are on the local network of your local university/institute/company.