Ok, so I think I have everything set up correctly. I'll test my cluster integration tomorrow. For now, I can see galaxy from my web browser.
First issue - When I go to User -> Login and try to log myself in (I've already registered myself), it looks like it works, but the browser get redirected really fast to another page, then again to the main page. The User menu never shows me as logged in as it does on the public usegalaxy.org site.
Is there a way to check that I'm actually logged in? If its not showing, then I assume something is wrong. Where do I look to debug this?
Ryan, congratulations on getting this far!
On Fri, Feb 18, 2011 at 3:52 PM, Ryan Golhar golharam@umdnj.edu wrote:
Ok, so I think I have everything set up correctly. I'll test my cluster integration tomorrow. For now, I can see galaxy from my web browser.
First issue - When I go to User -> Login and try to log myself in (I've already registered myself), it looks like it works, but the browser get redirected really fast to another page, then again to the main page. The User menu never shows me as logged in as it does on the public usegalaxy.org site.
Is there a way to check that I'm actually logged in? If its not showing, then I assume something is wrong. Where do I look to debug this?
Try hovering your mouse over the 'User' tab top right of the screen - if you see 'logged in as ....' at the top of the popup, then you are logged in. Otherwise not.
Also, if you have added your login email to the list of admin_users in universe_wsgi.ini (and restarted galaxy of course...), then you can tell you are logged in if you can see an 'Admin' tab - otherwise not.
Depending on your situation, you may want to consider using external authentication against (eg) an existing organizational ldap/active_directory or other authentication database and have apache pass the authentication headers through to a proxied galaxy. It's not trivial but the benefit is that users have single sign on - one less password to forget :)
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Ryan, congratulations on getting this far!
Thank you! :)
Ok, so I think I have everything set up correctly. I'll test my cluster integration tomorrow. For now, I can see galaxy from my web browser. First issue - When I go to User -> Login and try to log myself in (I've already registered myself), it looks like it works, but the browser get redirected really fast to another page, then again to the main page. The User menu never shows me as logged in as it does on the public usegalaxy.org <http://usegalaxy.org> site. Is there a way to check that I'm actually logged in? If its not showing, then I assume something is wrong. Where do I look to debug this?Try hovering your mouse over the 'User' tab top right of the screen - if you see 'logged in as ....' at the top of the popup, then you are logged in. Otherwise not.
yeah, I'm definitely not logged in. Something isn't taking.
Also, if you have added your login email to the list of admin_users in universe_wsgi.ini (and restarted galaxy of course...), then you can tell you are logged in if you can see an 'Admin' tab - otherwise not.
No, I haven't done anything with admin stuff yet.
Depending on your situation, you may want to consider using external authentication against (eg) an existing organizational ldap/active_directory or other authentication database and have apache pass the authentication headers through to a proxied galaxy. It's not trivial but the benefit is that users have single sign on - one less password to forget :)
I will, but first I want to get the default install working properly before doing anything else.
SO....I've removed the Apache proxy and am hitting galaxy directly on localhost:8080. Logging in still doesn't work. What else should I check? I'm connected to a mySQL database running on a different server. Could there be a problem there? paster.log doesn't seem to be much help in debugging this...
Ok, I don't know what happened with this...I reinstalled from scratch and i seems to be working now. I suspect perhaps because I started galaxy a few times before migrating to mysql. This time, I deleted everything, changed the config settings then started galaxy.
I'm now on to testing my cluster integration...so, I'm following this:
https://bitbucket.org/galaxy/galaxy-central/wiki/ISMB2010_GalaxyTutorial_3_R...
as my initial test. When I run the get flanks, I see the job get started on the cluster and errors out with the following error:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/new_operations/get_flanks.py", line 16, in ? from galaxy.tools.util.galaxyops import * File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 15, in ? from galaxy import util, jobs, model File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 4, in ? from galaxy import util, model File "/home/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 11, in ? import galaxy.datatypes.registry File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 6, in ? import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/data.py", line 7, in ? import metadata File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py", line 5, in ? from galaxy.web import form_builder File "/home/galaxy/galaxy-dist/lib/galaxy/web/__init__.py", line 5, in ? from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder, expose_api File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 18, in ? import helpers File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py", line 29 return (content if len(content) <= length else content[:length].rsplit(' ', 1)[0]+suffix) ^ SyntaxError: invalid syntax
If I submit the job script from the shell, the job runs, but when the web interface submits the job it doesn't. In both cases, its the galaxy user account so I don't think environment variables are to blame.
On 2/18/11 10:26 AM, Ryan Golhar wrote:
Ryan, congratulations on getting this far!
Thank you! :)
Ok, so I think I have everything set up correctly. I'll test my cluster integration tomorrow. For now, I can see galaxy from my web browser.
First issue - When I go to User -> Login and try to log myself in (I've already registered myself), it looks like it works, but the browser get redirected really fast to another page, then again to the main page. The User menu never shows me as logged in as it does on the public usegalaxy.org http://usegalaxy.org site.
Is there a way to check that I'm actually logged in? If its not showing, then I assume something is wrong. Where do I look to debug this?
Try hovering your mouse over the 'User' tab top right of the screen - if you see 'logged in as ....' at the top of the popup, then you are logged in. Otherwise not.
yeah, I'm definitely not logged in. Something isn't taking.
Also, if you have added your login email to the list of admin_users in universe_wsgi.ini (and restarted galaxy of course...), then you can tell you are logged in if you can see an 'Admin' tab - otherwise not.
No, I haven't done anything with admin stuff yet.
Depending on your situation, you may want to consider using external authentication against (eg) an existing organizational ldap/active_directory or other authentication database and have apache pass the authentication headers through to a proxied galaxy. It's not trivial but the benefit is that users have single sign on - one less password to forget :)
I will, but first I want to get the default install working properly before doing anything else.
SO....I've removed the Apache proxy and am hitting galaxy directly on localhost:8080. Logging in still doesn't work. What else should I check? I'm connected to a mySQL database running on a different server. Could there be a problem there? paster.log doesn't seem to be much help in debugging this...
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Fri, Feb 18, 2011 at 5:01 PM, Ryan Golhar golharam@umdnj.edu wrote:
Ok, I don't know what happened with this...I reinstalled from scratch and ...
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/new_operations/get_flanks.py", line 16, in ? ... File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py", line 29 return (content if len(content) <= length else content[:length].rsplit(' ', 1)[0]+suffix) ^ SyntaxError: invalid syntax
I deduce you're using Python 2.4, since that line of code is using the ternary operator added in Python 2.5 http://www.python.org/dev/peps/pep-0308/
Now that it has been reported I think it will be fixed to work with Python 2.4. However, the Galaxy team have indicated they will be dropping Python 2.4 (probably this year) so if I were you since this is a new setup I'd install Python 2.6 on this machine (Galaxy doesn't yet support Python 2.7).
Peter
Peter Cock wrote:
File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py", line 29 return (content if len(content) <= length else content[:length].rsplit(' ', 1)[0]+suffix) ^ SyntaxError: invalid syntax
I deduce you're using Python 2.4, since that line of code is using the ternary operator added in Python 2.5 http://www.python.org/dev/peps/pep-0308/
Now that it has been reported I think it will be fixed to work with Python 2.4. However, the Galaxy team have indicated they will be dropping Python 2.4 (probably this year) so if I were you since this is a new setup I'd install Python 2.6 on this machine (Galaxy doesn't yet support Python 2.7).
It was actually already fixed in 5019:39b40280ed6d, which was part of the last stable release.
--nate
Peter
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
galaxy-dev@lists.galaxyproject.org
-
Nate Coraor -
Peter Cock -
Ross -
Ryan Golhar