On closer inspection I'm not sure why you need the build-dependency on libmysql-java at all. The package builds fine without it. I wonder how igv loads the jdbc driver. It seems to make a runtime connection to a MySQL/MariaDB server though. Could also just be an option.
See line 83 in src/main/java/org/broad/igv/ui/action/LoadFromDatabaseAction.java So maybe you should remove the build-dependency and add libmariadb-java as a recommended or even suggested dependency instead. Markus
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