stevekm/IGV-snapshot-automator

Trying to run on a Mac

Closed this issue · 2 comments

afarahani951 commented

Hi,

This is absolutely amazing thank you guys for making this! I am trying to run it on my MacOS and getting stuck when it reaches the IGV command:

Running the IGV command...
/bin/sh: xvfb-run: command not found

Do you know if there is some alternative way to run the IGV command?

Thank you so much!

stevekm commented

My suggestion for Mac is to utilize the included Docker container / recipe and run it from there. xvfb-run is a helper script that is bundled with the X11 package in Linux distros (I think), I would not expect it to be available on Mac and I am not sure what the equivalent might be (perhaps something to do with XQuartz?)

stevekm commented

Also worth noting that if you are on Mac then you already have a GUI available and you can simply use the -nosnap option to create your sample .bat batch script (or write the script yourself) and run it from IGV in batch mode yourself, so you do not actually need IGV-snapshot-automator on Mac.