Hey I have another issue for you! :)

It's in the file lib/galaxy/webapps/community/controllers/repository.py

For some reason, when the  __add_hgweb_config_entry function tries to strip the repository_path from a possible leading './' it also removes the leading '/' in absolute paths. I could avoid the issue by commenting the code where './' are removed:

1032     def __add_hgweb_config_entry( self, trans, repository, repository_path ):
1033         # Add an entry in the hgweb.config file for a new repository.  An entry looks something like:
1034         # repos/test/mira_assembler = database/community_files/000/repo_123.
1035         hgweb_config = "%s/hgweb.config" %  trans.app.config.root
1036         #if repository_path.startswith( './' ):
1037         #    repository_path = repository_path.replace( './', '', 1 )
1038         entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path ) #.lstrip( './' ) )
1039         tmp_fd, tmp_fname = tempfile.mkstemp()

I'm really confused, but this seems to work for us.

Hope that can help
L-A


Le 28/11/2011 22:33, Greg Von Kuster a écrit :
The fix for the following config setting in community_wsgi.ini is now available in change set 6339:5db0da0007fc in our central repo.

require_login = True


On Nov 25, 2011, at 10:44 AM, Greg Von Kuster wrote:

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






___________________________________________________________
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




___________________________________________________________
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/
___________________________________________________________
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




<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 Von Kuster
Galaxy Development Team





Greg Von Kuster
Galaxy Development Team




___________________________________________________________
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



___________________________________________________________
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