stevekm/IGV-snapshot-automator

Instructions to get this working in cluster without X11

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ManavalanG commented

Figured I would share this here as this might help someone down the line. I use IGV in remote cluster where X11 is not available. I resolved this by using the instructions here - http://thedusseldorfer.blogspot.com/2013/09/remotely-plotting-with-igv-even-without.html. Note that this does not require sudo privileges.

Steps in brief:

  1. Download Xvfb.tgz and Xfnts.tgz from http://ftp.xfree86.org/pub/XFree86/4.8.0/binaries/
  2. Decompress them
  3. Run this ./Xvfb :0 -nolisten tcp -fp /path/to/lib/X11/fonts/misc &
  4. Set export DISPLAY=:0
  5. Now run IGV batch file: /path/to/igv.sh --batch /path/to/batch/file

I create IGV batch file using IGV-snapshot-automator, and with these batch files, I then create snapshots as described above. Hope this helps! If there is a better way to do this, or to get above Xvfb to work with xvfb-run and xdpyinfo without sudo privileges, please let me know.

stevekm commented

Thanks for this @ManavalanG

I was looking into similar things recently, trying to get this to work on macOS where X11 runs through XQuartz, but it seemed rather complicated and I never did get it working. In particular, I found that xvfb-run is simply a wrapper script to launch and manage the X11 server window; I pulled a copy of it from my HPC system and saved it here:

https://github.com/stevekm/IGV-snapshot-nf/blob/master/bin/xvfb-run_Centos6

Notably, this script, and other versions of the same I found online, seem to use several tools that are not available on macOS, though you may fare better on a Linux OS.

solivehong commented

@ManavalanG you can use anaconda install xvfb

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stevekm commented

as a followup to this, I have included a Singularity container recipe which you can use, if your cluster has Singularity available. https://github.com/stevekm/IGV-snapshot-automator/blob/d32f17893c261f2eb2b671291bec168dcb5a62be/Singularity

mewmewyahhey commented

@ManavalanG you can use anaconda install xvfb

I wonder which version of xvfb should I choose? I searched xvfb on the website of anaconda package and installed several of them, like xvfbwrapper, pytest-xvfb and xorg-x11-server-xvfb-cos7, but none of them has a command of "xvfb-run" and the tool didn't work.