Adding reference genome to session xml file

[mtr...@mindspring.com]

Hello

I have a script that generates simple igv session xml files and then creates links to these and writed them in an excel spreadsheet.

Here is an example of one such link

http://localhost:60151/load?file=http://demeter///scratch-large/3-monthly/GEDI2/CD118026583-01/1550623516/TMKD184100B002A/delivered/TMKD184100B002A-igv_session_file.xml

and here is the contents of the xml session file it links to

<?xml version="1.0" encoding="UTF-8"?>
<Global> genome="24505WT.fa" locus="24505WT.fa" version="3"
<Resources>
<Resource name="TMKD184100B002A align" path="http://demeter//scratch-large/3-monthly/GEDI2/CD118026583-01/1550623516/TMKD184100B002A/delivered/TMKD184100B002A-vs-24505WT.fa.sort.bam"/>
</Resources>
</Global>

The alignments pointed to in these files are often to references not previously loaded into my local igv, and so  they must be loaded to be able to see the sequence.  Currently I will enter the link (e.g. http://demeter/scratch-large/3-monthly/GEDI2/CD118026583-01/1550623516/TMKD184100B002A/delivered/24505WT.fa) to the reference in the "Load genome from URL" function in igv separately and manually.

Is there a way to include the loading of the genome in the session file and, if so, what is the syntax?

Thanks

Mark

[James Robinson]

Just set the value of the genome attribute to your url.  Be sure it is indexed, and has an ".fai" file in the same directory.

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