Thanks for all the time you've been spending on it.

Here is the config file for the toolshed:
http://pastebin.com/2ckCTqUa

And here is the config file for Galaxy:
http://pastebin.com/0FrzZsB4

Hoping it helps :)
L-A


Le 25/11/2011 17:21, Greg Von Kuster a écrit :

Apache front-ends are not my area of expertise ( Nate may be needed for this ), but if you send me your apache settings that your use for Galaxy, I may be able to help.  The tool shed uses the same static files as Galaxy, so they should be fine.  Possibly the only issue is rewrites for new paths (although again, I'm not very knowledgable on apache with regard to rewrites).  Here are the routes used in the tool shed if this helps.

    webapp.add_route( '/:controller/:action', action='index' )

    webapp.add_route( '/:action', controller='repository', action='index' )

    webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' )

On Nov 25, 2011, at 11:00 AM, Louise-Amélie Schmitt wrote:

Woohoo thanks a lot, it works! :)

Well almost, but at least we have something displayed. I guess there are some rewriterules missing (or just plain wrong) in our apache config file: No css or image are used and we get this error:

Not Found

The requested URL /repository/browse_categories was not found on this server.

Here are the rules:

RewriteEngine on
RewriteRule ^/toolshed$ /toolshed/ [R]
RewriteRule ^/toolshed/static/style/(.*) /home/galaxy/galaxy-dev/static/june_2007_style/blue/$1 [L]
RewriteRule ^/toolshed/static/(.*) /home/galaxy/galaxy-dev/static/$1 [L]
RewriteRule ^/toolshed/images/(.*) /home/galaxy/galaxy-dev/static/images/$1 [L]
RewriteRule ^/toolshed/upload/(.*) /home/galaxy/galaxy-dev/static/automated_upload/$1 [L]
RewriteRule ^/toolshed/favicon.ico /home/galaxy/galaxy-dev/static/favicon.ico [L]
RewriteRule ^/toolshed/robots.txt /home/galaxy/galaxy-dev/static/robots.txt [L]
RewriteRule ^/toolshed(.*) http://localhost:9009$1 [P]

I kinda guessed them from what we had for galaxy, but most likely completely failed at it... Maybe you could give us some guidelines for the toolshed apache config file, like there is for galaxy in the wiki?

Thanks,
L-A



Le 25/11/2011 16:44, Greg Von Kuster a écrit :

Set the following config setting in your community_wsgi.ini file to be False for now instead of True.  There's a bug in the shared Galaxy code base that produces the problem you see.  I'll get a fix in for this asap, but users are not required to login to use many of the features of the tool shed.  Let me know if you find additional issues - you're the first to set up your own tool shed, so you're in the position of having to iron out issues like this.  Thanks for all of your help!

# Force everyone to log in (disable anonymous access)

require_login = True

On Nov 25, 2011, at 9:38 AM, Louise-Amélie Schmitt wrote:

Well, the symlink is indeed not needed anymore, thanks for the fix.

However, the original error still stands. Here is the full output: http://pastebin.com/K5r6wd0A

Hope that helps
L-A


Le 25/11/2011 15:22, Greg Von Kuster a écrit :

Louise-Amelie,

The following setting is incorrectly included in community_wsgi.ini.sample - I've removed it in the latest change set.  I missed the setting in your community_wsgi.ini file - it should be removed from there as well, and I think things will work.  I apologize for this - there have been many changes to the config over the course of building the tool shed, and I obviously missed removing this old setting that is no longer used ( and, in fact now breaks things as we've found out ).  Very sorry for the inconvenience.

# Where templates are stored

template_path = lib/galaxy/webapps/community/templates

On Nov 25, 2011, at 8:48 AM, Louise-Amélie Schmitt wrote:

Here is the full log:
http://pastebin.com/qvB6UqxF


Le 25/11/2011 14:33, Greg Von Kuster a écrit :

That symlink should not be necessary.  Can you remove it and send me the complete paste log when you attempt to start your tool shed server?

On Nov 25, 2011, at 8:23 AM, Louise-Amélie Schmitt wrote:

Hello Greg,

This is precisely because we got the error that I added that section, like I mentioned earlier, but it didn't change anything. I will remove it again then.

Do you have any other idea that we could explore? Do you need other files?

Ah, I forgot to mention that at first start, it would complain about missing files so we created a symlink:
ln -s <galaxy_home>/templates/webapps/community <galaxy_home>/lib/galaxy/webapps/community/templates

Thanks,
L-A



Le 25/11/2011 14:07, Greg Von Kuster a écrit :

Hello Louise-Amelie,

I believe the problem is caused by the inclusion of the following settings in your community_webapp.ini file.  This sections should not be included in the tool shed config, so if you remove it things should work.  Let me know if you bump into other issues.  I apologize for the difficulty you've had in getting your own local tool shed up and running.  The tool shed wiki currently focuses on using the Galaxy public tool sheds, so I'll next add a section providing details for setting up your own.

# -- Display sites

 

# Galaxy can display data at various external browsers.  These options specify

# which browsers should be available.  URLs and builds available at these

# browsers are defined in the specifield files.

# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt

ucsc_display_sites = main,test,archaea,ucla

# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt

gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly,yeast_sgd

# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt

genetrack_display_sites = main,test

On Nov 25, 2011, at 3:01 AM, Louise-Amélie Schmitt wrote:

Hello Greg

Please find attached the file you asked for. Just in case, I also sent you the run_community.sh script we use to start the toolshed.

Thanks a lot,
Louise-Amélie


Le 25/11/2011 00:36, Greg Von Kuster a écrit :

Hello Louise,

Can you send me your community_wsgi.ini file?  I assume your copied it from community_wsgi.ini.sample, but somehow it looks like your configuration settings are attempting to start the Galaxy server instead of the tool shed server.  I should be able to sort it out for you by looking at your configuration file.

Thanks,

Greg Von Kuster

On Nov 24, 2011, at 10:34 AM, Louise-Amélie Schmitt wrote:

Hello Greg

We tried to run the toolshed like you explained (thanks a lot for the quick answer btw), it starts fine, but when we try to access it on the web, we get this error in the browser:

Server Error

An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)

In the logs, here is what we get:

Error -<type 'exceptions.AttributeError'>: 'Configuration' object has no attribute 'ucsc_display_sites'

URL: http://taiji/

File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__

app_iter = self.application(environ, start_response)

File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__

return self.application(environ, start_response)

File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__

return self.application(environ, start_response)

File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line 134 in __call__

trans = self.transaction_factory( environ )

File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 187 in<lambda>

self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) )

File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 207 in transaction_chooser

return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie )

File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 860 in __init__

self._ensure_logged_in_user( environ )

File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 420 in _ensure_logged_in_user

if self.app.config.ucsc_display_sites and self.request.path == display_as:

AttributeError: 'Configuration' object has no attribute 'ucsc_display_sites'

Since this name ringed a bell, I checked the universe_wsgi.ini and found this "Display sites" section. I therefore copied it and pasted it in the community.wsgi.ini file and uncommented the variables in this section. But when we tried again, we still get the same error.

What is confusing, is that after the error message, all the CGI, congifuration and WSGI variables are displayed, and in the configuration section we have this line:

ucsc_display_sites: 'main,test,archaea,ucla'

Did we miss anything? Where should we start searching for a possible error source?

Thanks,

L-A

Le 23/11/2011 16:11, Greg Von Kuster a écrit :

Hello Nicolas,

On Nov 22, 2011, at 11:04 AM, Nicolas Delhomme wrote:

Hi Greg,

I've been scanning the mailing list, but wasn't lucky enough to find the answer I was looking for.

Basically, we would be interested to have our own Galaxy Tool Shed in-house, to develop and test tools within our local Galaxy instance. What I'm thinking of, is to use the power of the tool shed to develop new algorithm, new tools, etc. that could be published afterwards.

This is great, but keep in mind that the intent of the tool shed (whether it is a local, proprietary tool shed or the public Galaxy tool shed) is to provide a vehicle for sharing tools (and tool-related objects like workflows, data types, etc) that are determined to be functional within a Galaxy instance.  So the primary use of a tool shed should be to enable sharing.  The tools themselves should be implemented within a development environment that includes a Galaxy instance, and when a tool is deemed functional, it can then be uploaded to the tool shed for sharing.

You can, however, tweak the primary intent of a tool shed to meet your needs.  In your case, it seems that you may be interested in using a local tool shed instance to share tools between developers during the development process.  If this is the case, then your approach can be one where a developer creates a repository on the local tool shed multiple developers can clone it.  The mercurial command line process for committing, pushing, pulling and updating can be used to share updates to the tool code by multiple developers throughout the process.

If a single developer is implementing the tool however, it may make more sense to not use the tool shed as part of the development process - just upload the tool when it is functional.

Because these would be sensitive material, we would not want to put them right away on the public test Tool Shed. Having a local Tool Shed instance would still be very helpful in releasing these tools to the community afterwards, as they would have been integrated and developed within that framework from the start.

This is a good approach.

Any pointers on how to achieve this are welcome as I'm not so familiar with the Tool Shed yet, e.g. would making a local clone of the tool shed repository be enough?

Make sure to read the tool shed wiki at http://wiki.g2.bx.psu.edu/Tool%20Shed.  I make sure to keep this up-to-date with the latest features of the tool shed.  You'll ffind, however, that there are some tool shed admin user features that have not yet been documented.  If you have any question, let me know.

The tool shed is included in the Galaxy distribution, so no additional cloning is necessary - it is just a different webpp from Galaxy itself.  It uses a different database from Galaxy, which you configure in the file community_wsgi.ini (the equivalent of universe_wsgi.ini for Galxy).  After you have the configuration settings as you want them, start up your local tool shed by:

%sh run_community.sh

Feel free to ask questions!

Thanks,

Nico

---------------------------------------------------------------

Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310

Email: nicolas.delhomme@embl.de

Meyerhofstrasse 1 - Postfach 10.2209

69102 Heidelberg, Germany

---------------------------------------------------------------

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greg@bx.psu.edu

___________________________________________________________

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___________________________________________________________

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:

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Greg Von Kuster

Galaxy Development Team

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<community_wsgi.ini><run_community.sh>___________________________________________________________
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/

Greg Von Kuster

Galaxy Development Team

greg@bx.psu.edu

Greg Von Kuster

Galaxy Development Team

greg@bx.psu.edu

Greg Von Kuster

Galaxy Development Team

greg@bx.psu.edu

___________________________________________________________
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/

Greg Von Kuster

Galaxy Development Team

greg@bx.psu.edu

Greg Von Kuster

Galaxy Development Team

greg@bx.psu.edu