Loading custom genomes in a session file

[Mark Rose]

Hello

I want to load a custom genome from a url (long with other files that reference that genome) in a session file.  I was unable to do that in IGV version  1 but I am wondering if this is possible with the latest version.  Here is what I unsuccessfully attempted:

<?xml version="1.0" encoding="UTF-8"?>
<Global> genome="https://<internet domain name>/project/NEDEL/igv_test/NGS22014_D7_UR276287862-refs.fa" locus="26130" version="3"
<Resources>
<Resource name="NGS22014_D7_UR276287862 align" path="http://<internet domain name>/project/NEDEL/igv_test/NGS22014_D7_UR276287862.all.fq-vs-construct_refs.fa.sort.bam"/>
<Resource name="NGS22014_D7_UR276287862 features" path="http://<internet domain name>/project/NEDEL/igv_test/NGS22014_D7_UR276287862-refs.gb"/>
</Resources>
</Global>

This does not load the specified genome but produces an error saying the bam file "does not contain any sequence names which match the current genome",  the current genome being the last one I selected in the GUI interface.  Is what I am trying to do still not possible, requiring instead that I first manually upload the custom genomes in the GUI, or is my code incorrect.

Thanks

Mark

[igv-help]

This looks correct.   I'll look into it tomorrow.

[robin...@gmail.com]

Well I can confirm the problem, it is a bug.   I will look into fixing this for the next release.  

[Mark Rose]

Thanks for looking. When will the next release be?

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[robin...@gmail.com]

Apologies I was mistaken, this is not an IGV bug, the problem is with your XML.  The good new is the fix is easy.   Change you second line to

<Global  genome="https://<internet domain name>/project/NEDEL/igv_test/NGS22014_D7_UR276287862-refs.fa" locus="26130" version="3">

[Mark Rose]

Got it.  Thanks for your help!

Mark

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