I'm now on to testing my cluster integration...so, I'm following this:
https://bitbucket.org/galaxy/galaxy-central/wiki/ISMB2010_GalaxyTutorial_3_RunningYourOwn
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: http://lists.bx.psu.edu/
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