Add batch command to overlay tracks

[jrobinso]

I am trying to take snapshots of the tracks loaded to IGV using command line. I am able to take them but I would like to overlay some tracks before taking the snapshots using command line igv. However, I am not able to find how to do it. Is there any option to overlay tracks via command line (or batch file)?

[CiaranOMara]

@jrobinso, I have this exact issue. Is there a batch command to overlay tracks?

[jrobinso]

Hi, no there is not. Batch commands are documented here: https://github.com/igvteam/igv/wiki/Batch-commands. I'm not sure why this was closed, will reopen but no ETA on when this could get done.

[malcook]

GroupOverlayBy <sampleAttribute> would be great

ancillary to #1083 would be GroupAutoscaleBy <sampleAttribute>

[jrobinso]

This is implemented, and will be in the next release sometime next week. An example script follows. Tracks to overlay can be specified byURL encoded track name, or by url or absolute file path of track file.

genome hg19
goto chr1
load https://www.encodeproject.org/files/ENCFF543IHG/@@download/ENCFF543IHG.bigWig
setColor 150,0,0 ENCFF543IHG.bigWig
load https://www.encodeproject.org/files/ENCFF039BJP/@@download/ENCFF039BJP.bigWig
setColor 0,150,0 ENCFF039BJP.bigWig
load https://www.encodeproject.org/files/ENCFF060LLG/@@download/ENCFF060LLG.bigWig
setColor 0,0,150 ENCFF060LLG.bigWig
overlay ENCODE%20Merged ENCFF543IHG.bigWig ENCFF039BJP.bigWig ENCFF060LLG.bigWig
snapshot merged.png
separate ENCODE%20Merged
snapshot separate.png
overlay ENCODE%20Merged%202 https://www.encodeproject.org/files/ENCFF543IHG/@@download/ENCFF543IHG.bigWig https://www.encodeproject.org/files/ENCFF039BJP/@@download/ENCFF039BJP.bigWig https://www.encodeproject.org/files/ENCFF060LLG/@@download/ENCFF060LLG.bigWig
snapshot merged_by_url.png