Hi all,

is there some way I can allow datasets (specifically bam files) that are annotated with a custom build to be displayed in a local IGV (assuming a genome with the same name was generated for IGV)?


I tried some things with display_applications/igv/bam.xml, but I couldn't get it to work properly. One challenge is to disable the filter for the local igv and the second challenge is to not do the build name mapping for custom builds. Here is what I tried, but didn't work (filter is still applied to local IGV):

<filter>
                #if $site_id.startswith( 'local_' )
                ${dataset.dbkey in $site_dbkeys}
                #end if
</filter>

<param type="template" name="site_organism" strip="True" >
                #if $bam_file.dbkey in $site_dbkeys
                $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
                #else
                $bam_file.dbkey
                #end if
</param>

Any help is greatly appreciated!

Best regards,
Sarah
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