load from server in IGV batch script

[boluda....@gmail.com]

Hi, 

I've been using the batch script, (as specified here https://igv.org/doc/desktop/#UserGuide/tools/batch/), for a while with great results. However, it is of great utility for me to load the Variations and Repeats annotations available from "load Server". I was wondering if it is possible and if so, which are the commands, to write on the batch script.

Any insight on this would be appreciated. Thanks!

[Helga Thorvaldsdottir]

There's no batch command for loading from server. However, if you know the URL to the annotations you want, you can use the load command to load it via URL. To find the URL, run IGV and then use Load from Server to load the annotations of interest. If you mouse over the track name you'll see the URL and it should also be recorded in the IGV log (in the igv folder in your user home). Just note that there are no guarantees that the annotation file will always be at that URL. It's possible that the location of hosted file can change in the future.

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