Question: Admin panel does not show up on interface
1
gravatar for katharina.schaufler
4 months ago by
katharina.schaufler10 wrote:

Hi there,

I know this problem has been discussed several times but the admin setup does not work for me. I've tried several possibilities, and read probably all threads on this topic. I'm trying to 'become' and admin, and followed the tutorial to do so.

That is,

  1. install the rep $ git clone -b release_17.05 https://github.com/galaxyproject/galaxy.git
  2. run galaxy $ sh run.sh
  3. stop galaxy $ crtl -c
  4. create a config/galaxy.ini file and add myself as an administrator $ sed 's/#admin_users = None/admin_users = myemailaddress.com/' config/galaxy.ini.sample > config/galaxy.ini (I also tried it without the # before admin_users)
  5. run galaxy $ sh run.sh
  6. stop galaxy $ crtl -c
  7. log onto the website with the exact same email address
  8. restart laptop

I tried several combinations, nothing works. The admin panel does not show up on the interface.

Suggestions would be highly appreciated.

Thanks, Katharina

galaxy • 219 views
ADD COMMENTlink written 4 months ago by katharina.schaufler10

Step 6 is not needed. The server needs to be up in order to log into the UI. Perhaps this was a typo? Also, I am not sure why step 8 was done, it is also not needed. Once the server is up, with admins already defined in galaxy.ini, log in to the UI and the account will become admin. Sometimes you'll need to refresh the browser window to clear the cache with "shift-reload" but that is not the usual case.

Also, "myemailaddress.com" should be something like myname@here.edu. It is not a ".com" URL but an email address. It can even be a disposable email address in a simple local set up for personal use. I use admin@admin.com (and others have their favorite defaults) all the time to keep it simple.

Punch line: there is probably a format problem with the galaxy.ini line for admin_users. Did you double check that the new galaxy.ini created (not the galaxy.ini.sample) contains the proper info? Leaving off the "#" from the sed command will result in a line that is not uncommented and it needs to be uncommented. You could edit the file directly with your editor of choice (Vim, Emacs, etc) to get the content right. The example sed command is to help people unfamiliar with unix get this basic admin config set up, but it relies on the original galaxy.ini.sample, without other changes or prior scripts/commands run against it first, and to be executed from the top level of Galaxy (don't cd into the config directory unless you also modify the paths in the sed command).

How to check the content of the admin_users line is in the same help section at http://getgalaxy.org.

Share the admin_users line from your galaxy.ini if you need more help. You can XXX out the email address for privacy.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson23k

Hi Jennifer,

I tried steps 6 and 8 because I read in previous threads that this helped in some cases. Same thing with the #. The bottom line is, I tried everything, also excluding these steps.

ADD REPLYlink written 4 months ago by katharina.schaufler10

Ok, good, I just wanted to double check. Try logging in now. The galaxy.ini content you shared is correct (or appears to be). That line should have no leading or trailing whitespace (spaces or tabs). Maybe double check that if there are still problems.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson23k

No, it's still the same ;-). I log out and back in- no admin. I've been trying this the whole day basically. Thanks for your help.

ADD REPLYlink written 4 months ago by katharina.schaufler10

Sorry to hear that none of this worked. This was a brand new instance, correct? You could try starting over. Problems can come up when something unintentional is altered. Isolating that can often take much more time, and be more frustrating, then starting with a fresh checkout. Let us know if you try and if it works or not. Should take about 10 minutes, max.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson23k

Hi Jennifer,

I just tried again with a totally new email address and account. It doesn't work. Am I missing sth major? Do I have to launch galaxy and then let it run for a long time before I add my email address? I've also tried changing my email address manually in the galaxy.ini file. Also, I put the galaxy directory in different locations- this didn't help either. Any other suggestions? I guess there is no way how you could add me as an admin?

Thanks, Katharina

ADD REPLYlink written 4 months ago by katharina.schaufler10
1

Hi Katharina

Sometimes, when I work with several galaxy servers running out of different directories, I modify the wrong 'galaxy.ini' file. A quick test, to double check whether you are modify the right file:

  • change "#brand = None" to "brand = Test"

  • restart your server, check the website: do you see: "Galaxy / Test" in the top left hand corner ?

Regards, Hans-Rudolf

ADD REPLYlink written 4 months ago by Hotz, Hans-Rudolf1.7k

Hi Hans-Rudolf,

I don't see "Galaxy / Test" in the corner. I only have one directory with galaxy though..

Thanks Katharina

ADD REPLYlink written 4 months ago by katharina.schaufler10

Well, this is a strong hint, that you are editing the wrong 'galaxy.ini' file or that (for whatever reason) this 'galaxy.ini' file is not read by the server.

Have you tried Jennifer's suggestion of starting over with a fresh checkout?

Hans-Rudolf

ADD REPLYlink written 4 months ago by Hotz, Hans-Rudolf1.7k

I have deleted the old version, started again new. Also tried with a different email address/a new registration. I only have this one galaxy folder, however. I looked at the galaxy.ini file manually, also located where it is manually. This is the only version within the only galaxy folder. But maybe I just also don't have any idea ;-). Sorry..

Best regards, Katharina

ADD REPLYlink written 4 months ago by katharina.schaufler10

You clearly have an idea, there is just some hidden typo/bug somewhere. Check that your galaxy.ini is named exactly like this and that it is in the config folder of your Galaxy. Do you see any errors/warnings in the log when starting up Galaxy?

ADD REPLYlink written 4 months ago by Martin Čech ♦♦ 4.2k

Yes, it's exactly galaxy.ini in the config folder (next to galaxy.ini.sample). There's one warning: WARNING:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config

Could this mean something?

ADD REPLYlink written 4 months ago by katharina.schaufler10
1

you can ignore this warning

Nevertheless, I am still convinced you are looking at two different galaxy servers: the one you access in your web browser, and the one you try to add your e-mail address as admin.

What happens, if you change the port in the 'galaxy.ini' file:

  • change "#port = 8080" to "port = 8090"
  • restart your server and follow the logs....you should now see a line with "serving on **:8090" instead of "serving on **:8080"
  • also, you now need to add the new port number to the URL in your web browser

Hans-Rudolf

ADD REPLYlink written 4 months ago by Hotz, Hans-Rudolf1.7k
0
gravatar for Martin Čech
4 months ago by
Martin Čech ♦♦ 4.2k
United States
Martin Čech ♦♦ 4.2k wrote:

All seems ok. Could you please paste here the exact line with admin_users as it is in config/galaxy.ini?

ADD COMMENTlink written 4 months ago by Martin Čech ♦♦ 4.2k

Thanks for your reply, do you mean this:

admin_users = xxx@xxx.de

ADD REPLYlink modified 4 months ago • written 4 months ago by katharina.schaufler10

This looks correct. Are you able to create a new account with this same email address now (within the UI)?

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson23k

You mean a new registration? It tells me that the email address already exists.

ADD REPLYlink written 4 months ago by katharina.schaufler10

If you log into it, are you now admin?

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

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