Display reference sequence and gff in one go to local IGV


On a custom tool I wrote, I produce 2 outputs:

  • A sequence I want to use as a reference genome for IGV
  • A gff file with the annotation of the previous sequence

I am able to display the sequence in IGV, then the gff by clicking on the “display with IGV (local)” button for both datasets, one after the other.

What I want to do is load the sequence as reference in IGV and add the gff in a single action, is this possible?

Additional question: Can I somehow force the “eye” display button of Galaxy to load the dataset directly into the local IGV? (To avoid people going to Dataset → Vizualize → display with IGV)

I have full control of the Galaxy instance if that helps.



maybe download both the sequence and annotation file to your computer and create visualization for the genome with the annotation file.

Reprogramming eye icon: I doubt users can do it. Plus, many users want the current function from the preview icon.

Kind regards,


Hi Igor,

Currently, users need to manually download and load both files into IGV due to the dynamic generation of the reference and GFF files by my tool.

What I am looking for is the possibility of linking the reference sequence in the metadata of the GFF file, sending everything to IGV using the “display in IGV” button, reducing the process to a single action from the user. I don’t know if it is possible?

I understand your point about the eye icon, changing its behaviour only for gff file could lead to more confusion.


Hi Jordi,
I am curious, can it be done through Custom Builds?
Have you considered JBrowse? It takes multiple files.
Kind regards,