It should just install with no issues.
If you have several domains pointing to the same server, I would use the Glassfish virtual hosting services to host them all in a single instance of the server. You'll save a lot of memory overhead doing that.
I would install glassfish, any place handy will do. /usr/local/glassfish, say.
By default you get the default domain, domain1: /usr/local/glassfish/domains/domain1
I would use that to test and make sure everything is working ok. But when I was done, I'd create a new domain someplace else, /usr/local/domains/yourdomain for example.
Use the asadmin --create-domain command to create your new domain, and don't forget the --domain-dir argument.
The reason you want to do this is that if you need to upgrade glassfish (say to the latest release for a bug or security fix), it's trivial to simply backup and reinstall the glassfish install without affecting your domain. You domain stays independent and safe, no copying files around, etc. The domain is pretty much stand alone and ignorant of the glassfish installation, and, in general, if you stay within the same version (i.e. GFv2), you won't need to change anything in your domain to work with the new version.
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