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....@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 <n...@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 > > > < > > http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way, > > > > > > > > _______________________________________________ > > > galaxy-user mailing list > > > galaxy-u...@lists.bx.psu.edu > > > http://lists.bx.psu.edu/listinfo/galaxy-user > > > > _______________________________________________ galaxy-dev mailing list firstname.lastname@example.org http://lists.bx.psu.edu/listinfo/galaxy-dev