Re: [galaxy-dev] [galaxy-user] Inquiring
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-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Dear All, We have a question regarding the Galaxy server. We installed a local version on our Linux machine and need move to a new place. The IP address will be changed. Could you please let me know if the server can be still used? I mean, we can use the new IP to open the home page of Galaxy and use it. For example if the new IP is "xxx.xxx.xxx.xxx", which is similar as before(I just replace the IP address). Do we need reset anything for Galaxy? Will the Galaxy use the fixed IP address in the system when it was installed? xxx.xxx.xxx.xxx:8080/root Looking forward to hearing from you. Best Wishes, Yan 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.
Dear Sir,
(1)We installed Galaxy, but recently the user can't registered and got
Yan Luo wrote: 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-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi Yan Assuming you have copied everything to the new server and you have changed the "host = xxx.xxx.xxx.xxx" line in the 'universe_wsgi.ini' file it should all work Regards, Hans-Rudolf On 10/31/2013 04:36 PM, Yan Luo wrote:
Dear All,
We have a question regarding the Galaxy server. We installed a local version on our Linux machine and need move to a new place. The IP address will be changed. Could you please let me know if the server can be still used? I mean, we can use the new IP to open the home page of Galaxy and use it. For example if the new IP is "xxx.xxx.xxx.xxx", which is similar as before(I just replace the IP address). Do we need reset anything for Galaxy? Will the Galaxy use the fixed IP address in the system when it was installed?
xxx.xxx.xxx.xxx:8080/root
Looking forward to hearing from you.
Best Wishes,
Yan
On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate@bx.psu.edu <mailto: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 > <http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,>
> _______________________________________________ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> > http://lists.bx.psu.edu/listinfo/galaxy-user
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi, Hans-Rudolf, Thanks for your response. We didn't build a new server, we just plan to change the IP address of the old server (The server will automatically get a new IP address when the physical address is moved). When server is started with new IP address, can we login directly using new IP address from client (web browser)? Could you please let me know if we only need change the IP address of file "universe_wsgi.ini"? Where is this file? Best Wishes, Yan Luo, Ph.D. Rockville, MD On Thu, Oct 31, 2013 at 12:05 PM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Yan
Assuming you have copied everything to the new server and you have changed the "host = xxx.xxx.xxx.xxx" line in the 'universe_wsgi.ini' file it should all work
Regards, Hans-Rudolf
On 10/31/2013 04:36 PM, Yan Luo wrote:
Dear All,
We have a question regarding the Galaxy server. We installed a local version on our Linux machine and need move to a new place. The IP address will be changed. Could you please let me know if the server can be still used? I mean, we can use the new IP to open the home page of Galaxy and use it. For example if the new IP is "xxx.xxx.xxx.xxx", which is similar as before(I just replace the IP address). Do we need reset anything for Galaxy? Will the Galaxy use the fixed IP address in the system when it was installed?
xxx.xxx.xxx.xxx:8080/root
Looking forward to hearing from you.
Best Wishes,
Yan
On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate@bx.psu.edu <mailto: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 > <http://int.ask.com/web?**siteid=10000861&webqsrc=999&l=** dis&q=By%20the%20way,<http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,>
> ______________________________**_________________ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.** psu.edu <galaxy-user@lists.bx.psu.edu>> > http://lists.bx.psu.edu/**listinfo/galaxy-user<http://lists.bx.psu.edu/listinfo/galaxy-user>
______________________________**_____________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/**search/mailinglists/<http://galaxyproject.org/search/mailinglists/>
Yan, The *universe_wsgi.ini* file is at the very top level of the galaxy install. This is the same directory location where you start the server. Hopefully you have found it! Jen Galaxy team On 10/31/13 10:52 AM, Yan Luo wrote:
Hi, Hans-Rudolf,
Thanks for your response. We didn't build a new server, we just plan to change the IP address of the old server (The server will automatically get a new IP address when the physical address is moved). When server is started with new IP address, can we login directly using new IP address from client (web browser)? Could you please let me know if we only need change the IP address of file "universe_wsgi.ini"? Where is this file?
Best Wishes,
Yan Luo, Ph.D. Rockville, MD
On Thu, Oct 31, 2013 at 12:05 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi Yan
Assuming you have copied everything to the new server and you have changed the "host = xxx.xxx.xxx.xxx" line in the 'universe_wsgi.ini' file it should all work
Regards, Hans-Rudolf
On 10/31/2013 04:36 PM, Yan Luo wrote:
Dear All,
We have a question regarding the Galaxy server. We installed a local version on our Linux machine and need move to a new place. The IP address will be changed. Could you please let me know if the server can be still used? I mean, we can use the new IP to open the home page of Galaxy and use it. For example if the new IP is "xxx.xxx.xxx.xxx", which is similar as before(I just replace the IP address). Do we need reset anything for Galaxy? Will the Galaxy use the fixed IP address in the system when it was installed?
xxx.xxx.xxx.xxx:8080/root
Looking forward to hearing from you.
Best Wishes,
Yan
On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate@bx.psu.edu <mailto:nate@bx.psu.edu> <mailto:nate@bx.psu.edu <mailto: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 >
<http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,>
> _______________________________________________ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> <mailto:galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>> > http://lists.bx.psu.edu/listinfo/galaxy-user
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jackson http://galaxyproject.org
Dear Jen, Thanks. Could you please let me know if we only need change the IP address of file "universe_wsgi.ini"? Then we can login by the new IP address. Is it? Best Wishes, Yan On Thu, Oct 31, 2013 at 3:45 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Yan,
The *universe_wsgi.ini* file is at the very top level of the galaxy install. This is the same directory location where you start the server.
Hopefully you have found it!
Jen Galaxy team
On 10/31/13 10:52 AM, Yan Luo wrote:
Hi, Hans-Rudolf,
Thanks for your response. We didn't build a new server, we just plan to change the IP address of the old server (The server will automatically get a new IP address when the physical address is moved). When server is started with new IP address, can we login directly using new IP address from client (web browser)? Could you please let me know if we only need change the IP address of file "universe_wsgi.ini"? Where is this file?
Best Wishes,
Yan Luo, Ph.D. Rockville, MD
On Thu, Oct 31, 2013 at 12:05 PM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Yan
Assuming you have copied everything to the new server and you have changed the "host = xxx.xxx.xxx.xxx" line in the 'universe_wsgi.ini' file it should all work
Regards, Hans-Rudolf
On 10/31/2013 04:36 PM, Yan Luo wrote:
Dear All,
We have a question regarding the Galaxy server. We installed a local version on our Linux machine and need move to a new place. The IP address will be changed. Could you please let me know if the server can be still used? I mean, we can use the new IP to open the home page of Galaxy and use it. For example if the new IP is "xxx.xxx.xxx.xxx", which is similar as before(I just replace the IP address). Do we need reset anything for Galaxy? Will the Galaxy use the fixed IP address in the system when it was installed?
xxx.xxx.xxx.xxx:8080/root
Looking forward to hearing from you.
Best Wishes,
Yan
On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate@bx.psu.edu <mailto: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 > < http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,
> _______________________________________________ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu <mailto: galaxy-user@lists.bx.psu.edu> > http://lists.bx.psu.edu/listinfo/galaxy-user
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Jennifer Hillman-Jacksonhttp://galaxyproject.org
Hi Yan, I do not know for 100% certain, but Hans gave advice recommending this and I trust his skill in this area greatly. It is certainly worth a try. If you have trouble, just write back in with details and be sure to stay on the galaxy-dev list as you are doing. This is where the core experience with running large local installs is concentrated. It is a holiday here in the US starting around now into early evening for those of us with small kids (Halloween) - so you may see some question delays for a few hours - many do this all before dark now (safer). But we'll BE BACK! :) Jen Galaxy team On 10/31/13 12:54 PM, Yan Luo wrote:
Dear Jen,
Thanks. Could you please let me know if we only need change the IP address of file "universe_wsgi.ini"? Then we can login by the new IP address. Is it?
Best Wishes,
Yan
On Thu, Oct 31, 2013 at 3:45 PM, Jennifer Jackson <jen@bx.psu.edu <mailto:jen@bx.psu.edu>> wrote:
Yan,
The *universe_wsgi.ini* file is at the very top level of the galaxy install. This is the same directory location where you start the server.
Hopefully you have found it!
Jen Galaxy team
On 10/31/13 10:52 AM, Yan Luo wrote:
Hi, Hans-Rudolf,
Thanks for your response. We didn't build a new server, we just plan to change the IP address of the old server (The server will automatically get a new IP address when the physical address is moved). When server is started with new IP address, can we login directly using new IP address from client (web browser)? Could you please let me know if we only need change the IP address of file "universe_wsgi.ini"? Where is this file?
Best Wishes,
Yan Luo, Ph.D. Rockville, MD
On Thu, Oct 31, 2013 at 12:05 PM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi Yan
Assuming you have copied everything to the new server and you have changed the "host = xxx.xxx.xxx.xxx" line in the 'universe_wsgi.ini' file it should all work
Regards, Hans-Rudolf
On 10/31/2013 04:36 PM, Yan Luo wrote:
Dear All,
We have a question regarding the Galaxy server. We installed a local version on our Linux machine and need move to a new place. The IP address will be changed. Could you please let me know if the server can be still used? I mean, we can use the new IP to open the home page of Galaxy and use it. For example if the new IP is "xxx.xxx.xxx.xxx", which is similar as before(I just replace the IP address). Do we need reset anything for Galaxy? Will the Galaxy use the fixed IP address in the system when it was installed?
xxx.xxx.xxx.xxx:8080/root
Looking forward to hearing from you.
Best Wishes,
Yan
On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate@bx.psu.edu <mailto:nate@bx.psu.edu> <mailto:nate@bx.psu.edu <mailto: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 >
<http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,>
> _______________________________________________ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> <mailto:galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>> > http://lists.bx.psu.edu/listinfo/galaxy-user
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-- Jennifer Hillman-Jackson http://galaxyproject.org
Hi Yan, As Hans mentioned, you should not need to update anything other than the `host` option in universe_wsgi.ini for most basic configurations (e.g. no proxy, database server (if any) is on the same server). Also, if you already have the host option set to 0.0.0.0, e.g.: host = 0.0.0.0 ...then you will not need to change anything. Specifying 0.0.0.0 will cause Galaxy to automatically bind to all available interfaces. --nate On Oct 31, 2013, at 3:54 PM, Yan Luo wrote:
Dear Jen,
Thanks. Could you please let me know if we only need change the IP address of file "universe_wsgi.ini"? Then we can login by the new IP address. Is it?
Best Wishes,
Yan
On Thu, Oct 31, 2013 at 3:45 PM, Jennifer Jackson <jen@bx.psu.edu> wrote: Yan,
The universe_wsgi.ini file is at the very top level of the galaxy install. This is the same directory location where you start the server.
Hopefully you have found it!
Jen Galaxy team
On 10/31/13 10:52 AM, Yan Luo wrote:
Hi, Hans-Rudolf,
Thanks for your response. We didn't build a new server, we just plan to change the IP address of the old server (The server will automatically get a new IP address when the physical address is moved). When server is started with new IP address, can we login directly using new IP address from client (web browser)? Could you please let me know if we only need change the IP address of file "universe_wsgi.ini"? Where is this file?
Best Wishes,
Yan Luo, Ph.D. Rockville, MD
On Thu, Oct 31, 2013 at 12:05 PM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote: Hi Yan
Assuming you have copied everything to the new server and you have changed the "host = xxx.xxx.xxx.xxx" line in the 'universe_wsgi.ini' file it should all work
Regards, Hans-Rudolf
On 10/31/2013 04:36 PM, Yan Luo wrote: Dear All,
We have a question regarding the Galaxy server. We installed a local version on our Linux machine and need move to a new place. The IP address will be changed. Could you please let me know if the server can be still used? I mean, we can use the new IP to open the home page of Galaxy and use it. For example if the new IP is "xxx.xxx.xxx.xxx", which is similar as before(I just replace the IP address). Do we need reset anything for Galaxy? Will the Galaxy use the fixed IP address in the system when it was installed?
xxx.xxx.xxx.xxx:8080/root
Looking forward to hearing from you.
Best Wishes,
Yan
On Thu, Feb 10, 2011 at 10:01 AM, Nate Coraor <nate@bx.psu.edu <mailto: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 > <http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,>
> _______________________________________________ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> > http://lists.bx.psu.edu/listinfo/galaxy-user
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (4)
-
Hans-Rudolf Hotz -
Jennifer Jackson -
Nate Coraor -
Yan Luo