Hi Yan,
I've again moved this back to the galaxy-dev list. Please reply to this list and not galaxy-user.
Yan Luo wrote:
Dear Nate,
Thanks for your quick response. I appreciate, it is very important for us to use it. We have problem recently.
(1) In fact, I can't find the file "paster.log". The problem is that recently we expanded our gluster(Linux sever) and did the rebalance that has some bugs. Some of files permission have been changed. So we can't use User/register righr now, when we tried, we got the sever error, do you have any idea how to fix it? (we can change the ownships/read and write permission for some files manually, but we don't know which files and where they are?)
If you are executing run.sh without the --daemon flag, the output will go to whatever terminal window you started Galaxy in, not to a file.
You'll want to make sure that all of the files under Galaxy's root directory are owned by a single user, which is the same user which starts and runs the Galaxy process.
(2) We want to reboot the Galaxy, should we first stop and start as follows? $ sh run.sh --stop $ sh run.sh
The full command to stop would be `sh run.sh --stop-daemon`, but that only applies if you originally started Galaxy with `run.sh --daemon`.
Is there any difference if I use "-daemon" flag? Last times, my colleague started using "./run.sh". How to stop it? If "$ sh run.sh --stop" doesn't work (I didn't try yet, ), how can I find the process (Linux) that is running by Galaxy and kill it?
The --daemon flag runs Galaxy in the background and redirects its output to paster.log. Without the --daemon flag, the process stays connected to the terminal in which you start it.
Since Galaxy wasn't originally started with the --daemon flag, you'll need to find the process, either by locating the terminal window in which it was started (possibly by your colleague) and then hitting Ctrl-C, or by using the `ps` command (e.g. `ps auxwww | grep python`) and killing the Galaxy process. It usually looks something like:
nate 18213 0.9 0.4 438844 146260 pts/7 Sl+ 10:47 2:30 python ./scripts/paster.py serve universe_wsgi.ini
So you would do:
% kill 18213
(3) Could you please let me know if there is a default administrator user/password for galaxy. I want to add an administrator user, how can I do that? According to the instruction, I will change a line of "universe_wsgi.ini" as follows. How can I set/get my password? admin_users = yan.luo@email.com
There is no default. Any users set in admin_uesrs will be administrators. If the account specified in admin_users does not yet exist, you can simply create it. Once created, that account will be an administrator.
(4) I found our "universe_wsgi.ini" contains the following setting, should I remove "#" before this line, stop and start galaxy? #allow_user_creation = True
No, True is the default setting so with it commented it is still set to True.
I plan to restart our galaxy, if it is possible, could you please let me know your phone #? I can call you sometime today, or if you prefer, I can give you my phone #.
Unfortunately, we don't have the resources for phone support. We'll be happy to help via email as much as possible.
--nate
Looking forward to hearing from you.
Best Wishes,
Yan Luo, Ph.D. NIH
On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor nate@bx.psu.edu wrote:
Hi Yan,
I've moved this discussion to the galaxy-dev list since it pertains to a local installation of Galaxy.
Responses to your questions follow, in-line.
Yan Luo wrote:
Dear Sir,
(1)We installed Galaxy, but recently the user can't registered and got
the
following error, how can we fix it?
Sever error An error occurred. See the error logs for more information.(To turn debug
on
to display ...).
Since debug = False in universe_wsgi.ini, you should be able to find a more detailed error message in the log file. If starting Galaxy with:
% sh run.sh --daemon
The default log file is 'paster.log' in Galaxy's root directory.
(2) Could you please let me know if there is any command to stop galaxy?
If starting with the --daemon flag (as above), you can use:
% sh run.sh --stop-daemon
If running in the foreground, you can use Ctrl-C to terminate the process. There is a recent bug whereby Ctrl-C is ineffective on some platforms under Python 2.6 - in this case you will have to kill/pkill the process manually. We are working on a fix for the latter.
(3) If I reset universe_wsgi.ini file and want to set an administrator user(I can add a line in the above file), how can I get the password?
Should
I stop galaxy(See question 2) first? then run "./setup.sh" and
"./run.sh".
setup.sh would have only been necessary prior to running Galaxy the first time, however, this step has recently been removed. If you are referencing documentation that still refers to setup.sh, please let us know so we can update it - I did notice this was still on the "Production Server" page, so I removed it from there.
You no longer need to run setup.sh at all.
(4) If I run "setup.sh", will a new file "universe_wsgi.ini" be
generated?
if I want to change this file,should I edit it before "run.sh" and after "setup.sh". Is it right?
setup.sh and its replacements in run.sh and the Galaxy application itself never overwrite files, they only create files from sample files if they do not exist.
(5) I read some of your docs, command "sh setup.sh"(sh run.sh) and "./setup.sh"(./run.sh), which one is correct under Linux?
Both syntaxes are effectively the same in most cases.
--nate
Looking forward to hearing from you.
Best Wises,
Yan Luo, Ph.D. NIH <
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