Hello Louise-Amelie, On Dec 1, 2011, at 4:08 AM, Louise-Amélie Schmitt wrote:

Yes this fixes the problem, it should work fine now :)

Thanks a lot!

Hehe, next issues:

1) When I have my repo created and I click on the "Upload files to repository", I get a Not found error in the browser: Not Found The requested URL /toolshed/upload/upload was not found on this server.

This is probably due to your apache rewrite rule: RewriteRule ^/toolshed/upload/(.*) /home/galaxy/galaxy-dev/static/automated_upload/$1 [L] Is this something proprietary you have set up on your local galaxy instance? Try removing it from your rewrite rules for your local tool shed.

2) When we try to access our local toolshed from our Galaxy instance, it appears in the "Accessible tool sheds" list along with your two public repos, but when we click on it, the "Valid repositories" list is empty. Is this a bug or does a repo have to actually contain files so it can appear in this list?

The list of valid repositories will only include repositories that have content that is valid for a Galaxy instance. These repositories are defined as either "valid" or in some cases "downloadable" (I'm working to replace the latter with the former). See the following sections of the tool shed wiki for details: http://wiki.g2.bx.psu.edu/Tool%20Shed#Repository_revisions:_downloadable_too... http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_...

3) Where should the hgweb.config be?

This file should be left in the Galaxy root install directory.

Actually, we have absolute paths since in the community_wsgi.ini we set the file_path option to an absolute path.

I advise against this - I'm fairly certain it will pose problems at some point. Tool shed paths should be relative. Here are some example entries in only of my local tool sheds: [paths] repos/test/filter = database/community_files/000/repo_1 repos/test/workflow_with_tools = database/community_files/000/repo_2 repos/test/heteroplasmy_workflow = database/community_files/000/repo_3

Thanks for your patience! L-A

Greg Von Kuster Galaxy Development Team greg@bx.psu.edu