Yes, everything is working fine.
Those notes are mostly for possible future improvement ideas.
Jennifer Jackson wrote, On 05/05/2011 01:52 PM:
Sorry for the delay in reply. Did you get help/resolve the problems you were having? Or
do you still need help?
On 3/30/11 3:12 PM, Assaf Gordon wrote:
> Hi all,
> It's been a long while since I had to install a fresh production galaxy server,
and I can offer some tips or requests for minor improvements (but to give credit were
it's due - installation is much smoother now, and DRMAA works great with SGE out of
> These are just minor annoyances, but they can help make new installations easier.
> 1. Debugging REMOTE_USER issues.
> The mix of apache + authentication + non-root URL + load balancing is a killer.
> googling "mod_rewrite + mod_auth" shows that I'm not the only one
having problems with it...
> Adding those two lines in
"./lib/galaxy/web/framework/middleware/remoteuser.py", line 79 is a wonderful
debugging tool, which enables you to see what Apache is passing on to Galaxy:
> for k,v in environ.items():
> sys.stderr.write ( "%s:\t%s\n" % ( k, v ) )
> I needed to print all environment variables (not just HTTP_REMOTE_USER) so I could
debug mod_rewrite's variables setup.
> If there was an easy way to enable this debug from the INI file it would be a great
> 2. The file name "universe_wsgi.ini" is hard-coded in several places.
> Most of them are python scripts (like cleanup, ampq, etc.), but one is
> Not a real problem, except that in the "WebApplicationScaling" wiki page
it's kind of implied that "universe_wsgi.ini" is not used any more after
creating the two separated ini files (universe_wsgi.runner.ini and
> If you rename "universe_wsgi.ini" instead of copying it, galaxy will simply
not start, even if given a different INI file name.
> So the best recommendation (in the documents) would probably be to maintain three
identical INI files,
> except for the "[server:main]" part of each (and the
"enable_job_running = False" in the runner).
> Most importantly, make sure that the database connection string is identical in all
> As a side node, the "cp" command in the "WebApplicationScaling"
wiki page is incorrect (you can't copy one file into two files).
> It'll also be good to mention that the cleanup scripts will always use
"universe_wsgi.ini" regardless of what the galaxy server is using.
> 3. Saving SGE/PBS/DRMAA shell scripts if "debug=TRUE" in the
jobrunner's INI file - this one is a gem, too bad I discovered it too late.
> If only it was documented :)
> 4. INI keys that accept multiple comma separated values (e.g.
"admin_users") are sensitive to white space.
> admin_users = firstname.lastname@example.org,email@example.com
> works fine, but:
> admin_users = gordon(a)cshl.edu , foobar(a)cshl.edu
> will not work (spaces around the comma).
> Same thing with "ucsc_display_sites":
> ucsc_display_sites = cshl,main
> will work (and display both "cshl" and "main"),
> ucsc_display_sites = cshl, main
> will display only "cshl" (because "main" is " main"
with a space).
> It's probably easier to document it than to fix it, but either will do.
> 5. There's no "ensembl_display_sites" in the INI, so disabling the
"display at ensembl" link (for BAM files, etc.) requires commenting out the
corresponding "<display>" tag in "datatypes_conf.xml", whereas
for other servers (gbrowse,ucsc) it's enough to comment out the
"ucsc_display_sites" in the INI.
> 6. For galaxy servers running inside an intranet without access to the main/test UCSC
Genome browser server,
> and want to use a local mirror (this might be an obscure setup but that's what I
> disabling both "main" and "test" in
"ucsc_display_sites" will disable the authenticated user bypass, because
"remouteuser.py" have them hard-coded before setting "self.allow_ucsc_main
> I needed to patch and add "cshl" as a third option - this is kind of ugly.
> Two development issues not related to production server installation:
> 1. Debugging complex cheetah templates is very hard. If you have good tricks (beyond
#slient and #breakpoint) - examples would be appriciated.
> If there's a way to see the compiled cheetah code which produced the error - it
would be great.
> One problem is that the error is always reported without a line number (I guess
because it's first converted into a string) and without the offending tag.
> 2. I only half-understand the new "tool_data_table_conf.xml" mechanism - is
it explained somewhere ?
> Looks quite complicated, especially adding in-lined lamba for reading the
"__app__" global variable inside the cheetah code of each tool :(
> And user interface quirks:
> 1. when managing workflows, the "configure your workflow menu" page is a
bit uninformative: there's no title, header, instruction or anything else, and the
button says "Submit Query" which doesn't mean much ("Update Workflow
Menu" would be better).
> If you click on "configure your workflow menu" and you don't have any
workflows, the page is down right mysterious .
> 2. JQuery Tipsy balloons - please make them go away.
> Or, make the appearance delay changeable in the INI file (to something like 600
seconds :) ).
> As always, grumbling aside, galaxy is GREAT! so keep up the good work.
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