On Mar 23, 2012, at 10:09 AM, Daniel Sobral wrote:

The path I defined on shed_tool_conf.xml should be writable. In fact, I can install repositories from your toolsheds (galaxy main or galaxy test) with no problems. I actually used the galaxy test toolshed to add my own repositories as a workaround of having my own toolshed! The path on shed_tool_conf is outside the galaxy-dist.

Ok, then could it be your apache rewrite rules? It's certainly something in your proprietary environment, but I have no idea what, in particular.

The error seems to come from my toolshed. I'm running the galaxy and the toolshed under the same galaxy clone, but I think this is the intended usage, no?

Yes, this is fine to do, but you should not be using the same database.

Thanks for the help, Daniel

On 03/23/2012 01:43 PM, Greg Von Kuster wrote:

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Hi Daniel,

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On Mar 22, 2012, at 11:21 AM, Daniel Sobral wrote:

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Hi Greg,

This is the output I get in the toolshed log: " Firefox/10.0.2" 172.22.50.249 - - [22/Mar/2012:15:11:50 +0100] "GET /toolshed/repository/install_repository_revision?repository_id=190cd6004dde15fd&changeset_revision=22619d71daa6&webapp=galaxy HTTP/1.1" 302 - "

What I read from this is that someone tried to access the repository to install the tool, which is correct.

You should be seeing something like this instead, so it looks like the repository is not being cloned.

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Clicking the install button when browsing the tool shed from Galaxy will produce something like the following in your tool shed paster log:

128.118.200.161 - - [16/Mar/2012:09:48:30 -0400] "GET /repos/test/filter?pairs=0000000000000000000000000000000000000000-0000000000000000000000000000000000000000&cmd=between HTTP/1.1" 200 1 "-" "mercurial/proto-1.0" 128.118.200.161 - - [16/Mar/2012:09:48:30 -0400] "GET /repos/test/filter?cmd=heads HTTP/1.1" 200 41 "-" "mercurial/proto-1.0" 128.118.200.161 - - [16/Mar/2012:09:48:30 -0400] "GET /repos/test/filter?cmd=changegroup&roots=0000000000000000000000000000000000000000 HTTP/1.1" 200 - "-" "mercurial/proto-1.0" 128.118.200.161 - - [16/Mar/2012:09:48:30 -0400] "GET /repos/test/filter?cmd=capabilities HTTP/1.1" 200 79 "-" "mercurial/proto-1.0" 128.118.200.161 - - [16/Mar/2012:09:48:30 -0400] "GET /repos/test/filter?cmd=listkeys&namespace=bookmarks HTTP/1.1" 200 - "-" "mercurial/proto-1.0" 128.118.200.161 - - [16/Mar/2012:09:48:31 -0400] "GET /get_tool_versions?name=filter&owner=test&changeset_revision=8ab8044881c6&webapp=galaxy HTTP/1.1" 200 - "-" "Python-urllib/2.6" And then I get this in the galaxy server log: " 172.22.50.249 - - [22/Mar/2012:15:11:56 +0100] "GET /galaxy/admin_toolshed/browse_repositories?status=error&message=abort%3A+HTTP+Error+404%3A+Not+Found%0A%3Cbr%2F%3E HTTP/1.1" 200 -

This confirms that your repository is not cloned. Are you using the default file named shed_tool_conf.xml for this? What is the value of the "tool_path" attribute in the <tool> tag of this file? Is that directory writeable by the user that start up the Galaxy server?