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: >> Hi Daniel, >> >> >>>> On Mar 22, 2012, at 11:21 AM, Daniel Sobral wrote: >>>> >>>>> 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. >> >> >>>>>> 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? >> > ___________________________________________________________ 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/
