Question: How config the admin menu (adding an administrator in galaxy / biolinux)
1
gravatar for alfonso.cervantes
3.5 years ago by
alfonso.cervantes10 wrote:

Dear all,

Currently i have bio-linux with galaxy installed locally, and i can't configure the administrator.

So.

Galaxy is installed into the folder galaxy server and when i try to edit the file "universe_wsgi.ini" i see a file with the name "universe_wsgi.ini.dpkg_old", then i rename this file by "universe_wsgi.ini" and edit with sudo command:

# Administrative users - set this to a comma-separated list of valid Galaxy
# users (email addresses).  These users will have access to the Admin section
# of the server, and will have access to create users, groups, roles,
# libraries, and more.  For more information, see:
# http://wiki.g2.bx.psu.edu/Admin/Interface
admin_users = alfonso.cervantes@cieni.org.mx

and I still do not display the administrator menu

what can i do?

AJCR

 

 

local config biolinux • 4.1k views
ADD COMMENTlink modified 17 months ago by Re7ab0 • written 3.5 years ago by alfonso.cervantes10

Hi there!

Thanks a lot for the information.

  I have one more question. Do you know about any tutorial for galaxy in bio-linux?

Thank you for all.

AJCR

ADD REPLYlink written 3.5 years ago by alfonso.cervantes10

Please create a new question so we can keep them focused.

ADD REPLYlink written 3.5 years ago by Martin Čech ♦♦ 4.2k
8
gravatar for Dannon Baker
3.5 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

Bio-linux works a little differently.

To add an administrator to a Bio-linux based galaxy server, you should be able to run a command like:

sudo galaxy-add-administrator "foo@foo.com"

 

If you need to modify universe_wsgi.ini directly, the file you're looking for exists as a series of composites you'll find at /etc/galaxy-server/universe_wsgi.d/*.ini

 

ADD COMMENTlink written 3.5 years ago by Dannon Baker3.7k

Thank you so much. I was trying to setup my local galaxy on a BioLinux 8 for 3 days and no matter which admin access line I edited in galaxy.ini or tool_shed.ini I couldn't gain access.

This solved the problem in a heartbeat.  (sudo galaxy-add-administrator "foo@foo.com")

Cheers.

ADD REPLYlink written 2.6 years ago by msalavati0
1
gravatar for Suzanne Gomes
2.9 years ago by
Suzanne Gomes120
Canada
Suzanne Gomes120 wrote:

Hi again,

Managed to fix the problem. It turns out that the galaxy-add-administrator file was in /usr but outside of /sbin. So I moved it into /sbin and then the command worked just fine. This may be really obvious, but I hope it helps anyone else with minimal computer skills that may be having the same problem...

Thanks everyone for the advice

 

ADD COMMENTlink written 2.9 years ago by Suzanne Gomes120
0
gravatar for Suzanne Gomes
2.9 years ago by
Suzanne Gomes120
Canada
Suzanne Gomes120 wrote:

I am also trying to configure administrator on a biolinux system. I put in the above command with my email address (I tried with and without the quotation marks as not sure if they were necessary). Either way, I get this:

sudo: galaxy-add-administrator: command not found

Any advice? 

ADD COMMENTlink written 2.9 years ago by Suzanne Gomes120
0
gravatar for alfonso.cervantes
2.9 years ago by
alfonso.cervantes10 wrote:

Hi Suzanne!

Then... you put the two points ":"  in the instruction?

You only need to put the next command in the terminal:

sudo galaxy-add-administrator email@xxx.com

Regards! 

ADD COMMENTlink written 2.9 years ago by alfonso.cervantes10
0
gravatar for Suzanne Gomes
2.9 years ago by
Suzanne Gomes120
Canada
Suzanne Gomes120 wrote:

No, I didn't add the ':'. The command I typed was sudo galaxy-add-administrator email@xxx.com. The computer added the ':' when it told me that the command was not found. 

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Suzanne Gomes120
0
gravatar for alfonso.cervantes
2.9 years ago by
alfonso.cervantes10 wrote:

uhm... I have a question!

if you put in the terminal galaxy-add and then push the key Tab, is autocomplete the command?

ADD COMMENTlink written 2.9 years ago by alfonso.cervantes10
0
gravatar for Suzanne Gomes
2.9 years ago by
Suzanne Gomes120
Canada
Suzanne Gomes120 wrote:

Hmm.. no, it doesn't autocomplete. Nothing happens.

ADD COMMENTlink written 2.9 years ago by Suzanne Gomes120

What version of biolinux are you using?  Perhaps this command has changed since I last used it, I'll check.  I'm downloading biolinux 8 now to test, but it'll take a while it looks like; I believe I wrote the previous answer based on biolinux 7.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Dannon Baker3.7k

So I finally finished downloading the new biolinux 8, and as the 'manager' user, this should definitely be on your path.  Can you verify your biolinux version, and that /usr/sbin/galaxy-add-administrator not exist for you?

ADD REPLYlink written 2.9 years ago by Dannon Baker3.7k
0
gravatar for Suzanne Gomes
2.9 years ago by
Suzanne Gomes120
Canada
Suzanne Gomes120 wrote:

Yes, it is biolinux 8. I went into /usr and found the file galaxy-add-administrator. It is in green text, while the rest are in blue. Does this mean something? It also says -rwxr-xr-x. 

Thanks for your help.. I don't really know anything about running stuff on the command line so it's hard for me to pinpoint what's going wrong.

ADD COMMENTlink written 2.9 years ago by Suzanne Gomes120

I'm not sure what's going on with your biolinux install (and am certainly not an expert on it), but can you execute galaxy-add-administrator using the full path?   So, `sudo /usr/sbin/galaxy-add-administrator foo@foo.com` ?

ADD REPLYlink written 2.9 years ago by Dannon Baker3.7k

I actually managed to solve this issue (somehow that response ended up near the top of the thread). Turns out the file wasn't in the right place for some reason (it was in /usr but outside of /sbin). Thanks for your help though :)

ADD REPLYlink written 2.9 years ago by Suzanne Gomes120
0
gravatar for Re7ab
17 months ago by
Re7ab0
Khartoum
Re7ab0 wrote:

You may need to remove the # in front of admin_user...If forgot to do so! Thanks,,,

ADD COMMENTlink written 17 months ago by Re7ab0
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