Basic questions welcome!
When you run
run.sh in the terminal, it effectively ‘takes over’ your terminal window, in that (unless you do other tricky things), the fate of Galaxy is tied to that window until you stop the process (by pressing control + C, for example, which will gracefully kill off Galaxy) or close the terminal window, ending the session.
as I understand it, you’ve copied galaxy.yml.sample to galaxy.yml – if galaxy.yml is in the
config directory where you found the sample, then it should be read on Galaxy start. Galaxy searches this directory for all relevant files and reads the info contained but, since you copied the sample, it will contain the defaults it is already running with until you make modifications.
i assume that you want to add your username to the admin list, so the user you created is an administrator with all the power and privilege the role comes with. to do that, all you need is an
admin_users entry in
galaxy portion of galaxy.yml that looks like this:
<some other entries, maybe>
the copied sample will have
admin_users in the file (somewhere after
galaxy:, probably commented out with a ‘#’). you can just look for that entry in the file (admin_users), remove the ‘#’, then put your email address you used to register with after the colon (my default has ‘null’ that i replaced with my email address).
closing and opening the web page will not impact the state of the Galaxy process, so you can open and close web pages to your heart’s content. Since your Galaxy and terminal are tied together (in 'nix parlance, your job is in the foreground of your terminal session), you will need to keep your terminal window open so as not to end the session and the Galaxy process. if you want to make it a background process that ‘just happens,’ there are many fine options, though it does get a bit technical (as do most administration tasks, heh)
let me know if you have further questions, need clarification, or if i misunderstood your needs!