IGV over SSH?
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17 months ago
Richard ▴ 580

Hi folks,

As are many of us I am working from home and using IGV is a bottleneck in my remote workflow. I'm trying to find the best way to quickly access a high-res IGV session.

My Bam files are on a remote server that I can access via ssh/scp.

The fastest way for me to view a bam file with IGV is to SSH with X forwarding and fire up IGV on the server. This is workable, but the resolution is much lower than I am used to from running IGV locally and makes really poor screenshots.

Another, much better looking option is to copy BAM files from the server and run IGV locally. This works if I really need a good screenshot, but of course I need to copy a lot of data locally which doesn't scale at all on my local laptop.

My question: Is there a way to configure IGV such that it will allow me to access BAM files over SSH in my local IGV session?

IGV SSH remote • 1.3k views
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makes really poor screenshots.

You should be able to export screens you need rather than using screenshots.

File --> Save Image --> Saves a snapshot of the IGV window to a graphics file, omitting the menu bar and tool bar. Specify the image file format by setting the filename extension in the file save dialog to .png, .jpeg, .jpg, or .svg.

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Is there a way to do this in a batch file? The only command seems to be snapshot, which does not exclude the menu/tool bars.

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See this (space added after https to prevent gist rendering: https ://gist.github.com/dfjenkins3/5c6dc1e55e78fa17b931 and https ://gist.github.com/stevekm/ac76c0c2fa4ee89db8ce2421cc6fbffc

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Thank you, I was mistaken - snapshot saves an image without the menu/tool bars.

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4
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17 months ago

use a virtual directory with sshfs (FUSE) ?

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Would this still not scp the entire BAM before letting IGV read the file? Or does SSHFS stream files on demand?

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it's random access through ssh

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I see. Thank you, Pierre. This will be really useful to me too.

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