Using remote-genomes.txt vs. user-defined-genomes.txt

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Benjamin Yeh

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Apr 29, 2025, 6:20:50 PMApr 29

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Dear IGV team,

When using custom genomes, when should I use remote-genomes.txt versus user-defined-genomes.txt?

Searching for those hard-coded filenames in the IGV GitHub repo seemed to indicate that IGV first looks for remote-genomes.txt, and then if that file does not exist, looks for user-defined-genomes.txt. Is that correct?

https://github.com/igvteam/igv/blob/bbded2ba092e7b1d02bc738fd47c8b921df1ca31/src/main/java/org/broad/igv/ui/commandbar/GenomeListManager.java#L402-L415

Would it be possible to update the IGV desktop documentation with information about using remote-genomes.txt and user-defined-genomes.txt?

Thanks for developing and maintaining the IGV software!

Ben

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IGV and system information

IGV version: 2.19.4
Java(TM) SE Runtime Environment (build 22.0.2+9-70)
Operating system: Red Hat Enterprise Linux release 9.3

igv-help

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Apr 30, 2025, 4:26:01 PMApr 30

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You shouldn't edit those files. Just load the .json file for your genome via the Genomes menu.