Hello,
I installed local galaxy, and ran in terminal (sh run.sh command). I left it for 24 hours, and the terminal still did not finish running (ie. reset so i can perform a new command), however i clicked the link for the local host and opened Galaxy webpage. I registered an account, and then opened the terminal window and performed
$ cp config/galaxy.yml.sample config/galaxy.yml
I closed the webpage and killed the galaxy job id in the terminal window. Now I can’t re-open Galaxy
Alexa
Galaxy is up as long as you don’t kill its process, which you seemingly did. Either leave the Galaxy running in the terminal, or manage it some other way e.g. using supervisor https://training.galaxyproject.org/training-material/topics/admin/tutorials/systemd-supervisor/slides.html#1
hello!
to add to Marten’s answer, the run.sh script is meant to run in your terminal window, scrolling server output for a human to monitor. there are ways to run it in the background such as using an ampersand (i.e., ./run.sh > some_log_file 2>&1 &) explained here, but to speak to your question:
how did you close the job – ctrl+c? kill -9 <pid>? what happens when you try to re-open (re-reun run.sh in the terminal?) Galaxy?
Hello,
I was not sure if terminating it was required to re-start it after configuration. I listed things running in the directory using ps -ax and then just wrote in kill . When I try to re-run the run.sh command, it lists many “requirements already satisfied” lines, followed by
And then when I click on the http://localhost:8080 link, Galaxy does not open.
Do I need to re-install?
I am not experienced with bioinformatics, my end goal here is to become an admin so I can add tools that I need to Galaxy.
Try starting over and following these instructions:
if you type:
ps -aux | grep uwsgi
…my guess is you’ll see uwsgi/galaxy processes that look something like this:
usr 25558 0.2 0.0 1422448 270768 pts/2 S+ 09:05 0:16 /home/lab/galaxy/.venv/bin/python .venv/bin/uwsgi --yaml /home/lab/galaxy/config/galaxy.yml --module galaxy.webapps.galaxy.buildapp:uwsgi_app() --virtualenv /home/lab/galaxy/.venv --pythonpath lib --buffer-size 16384 --static-map /static/style=/home/lab/galaxy/static/style/blue --static-map /static=/home/lab/galaxy/static --static-map /favicon.ico=/home/lab/galaxy/static/favicon.ico --static-safe /home/lab/galaxy/config/plugins/visualizations --static-safe /home/lab/galaxy/config/plugins/interactive_environments --die-on-term --hook-master-start unix_signal:2 gracefully_kill_them_all --hook-master-start unix_signal:15 gracefully_kill_them_all --py-call-osafterfork
run.sh is a launcher script, so its possible you killed the executing script, but not the underlying galaxy processes launched (which is what is shown after running the command above). you can kill them by observing the PID (second column in the example, 25558, but your numbers will be different) and running kill -9 <the PIDs you found>.
In the future, if you launch run.sh classically on the terminal (as you did before, where it takes up your whole terminal to print output), ctrl+c will gracefully exit both the launching scripts and the underlying Galaxy processes.
Thank you both for your help, so I just re-started, I have it running in the terminal window and have access to to the webpage. I created the username and now have a file in the directory called galaxy.yml.
I just want to be clear about the next steps so I don’t mess this up. But the next command should be:
$ cp config/galaxy.yml http: 0. 0. 0. 0
does this allow me to access the configured file through the webpage?
I am not sure exactly how I add my username to this file.
Then I just close the webpage but not the terminal windowm re-open the webpage, login and I should be an admin? Do I need to keep the terminal window open to use Galaxy on the webpage or I can close it as long as I don’t kill it like last time? (Sorry for basic questions, very new at this, appreciate your help)
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:
galaxy:
<some other entries, maybe>
admin_users: whatever.your.email.is@address.com
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!
Thank you so much for your reply, that was very helpful!
I added my email to the .yml file. Just to be clear, at this point I want to close the webpage and gracefully kill galaxy (just go to terminal window and type ctrl c), and then re-start (re-run the sh run.sh command) to see the configuration changes?
Yes.
It is usually better to shut down Galaxy first before making any configuration changes line-command, but this should work since this specific change was minimal. Shut down first next time to avoid problems.
Hello,
Okay I will keep that in mind for next time,
I see the admin bar at the top
Thank you both for your help, I really appreciate it!!