Local Toolshed misbehaviours?
Hello, I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool. In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the tool, it gives me: abort: HTTP Error 404: Not Found . I can install tools from the main galaxy toolshed without problems. I've also uploaded a test tool to the test toolshed server http://testtoolshed.g2.bx.psu.edu and I could install the tools in my galaxy server. Any ideas of what I may be doing wrong here with my toolshed server?
From the galaxy Toolshed wiki I cannot see anything to give me a clue about what's going on...
Thanks, Daniel
Hi Daniel, What does your tool shed paster log say when you get the 404 error trying to install? You can see the paster log by running the following from your Galaxy installation directory when your tool shed is running. tail -f community_webapp.log Greg Von Kuster On Mar 16, 2012, at 4:34 AM, Daniel Sobral wrote:
Hello,
I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool.
In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the tool, it gives me: abort: HTTP Error 404: Not Found .
I can install tools from the main galaxy toolshed without problems. I've also uploaded a test tool to the test toolshed server http://testtoolshed.g2.bx.psu.edu and I could install the tools in my galaxy server.
Any ideas of what I may be doing wrong here with my toolshed server?
From the galaxy Toolshed wiki I cannot see anything to give me a clue about what's going on...
Thanks, Daniel
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Hi Greg, The paster log from the toolshed server does not tells me much: 172.22.50.249 - - [16/Mar/2012:12:27:31 +0100] "GET /toolshed/repository/preview_tools_in_changeset?repository_id=2bccd98f7ba1e82a&changeset_revision=a42c4c034c26&webapp=galaxy HTTP/1.1" 200 - "http://myserver/toolshed//repository/browse_valid_repositories?galaxy_url=http://myserver/galaxy/&webapp=galaxy" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 172.22.50.249 - - [16/Mar/2012:12:27:44 +0100] "GET /toolshed/repository/install_repository_revision?repository_id=2bccd98f7ba1e82a&changeset_revision=a42c4c034c26&webapp=galaxy HTTP/1.1" 302 - "http://myserver/toolshed/repository/preview_tools_in_changeset?repository_id=2bccd98f7ba1e82a&changeset_revision=a42c4c034c26&webapp=galaxy" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" But the galaxy paster indicates a failure: 172.22.50.249 - - [16/Mar/2012:12:28:03 +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 - "http://myserver/galaxy/admin_toolshed/install_repository?tool_shed_url=http://myserver/toolshed/&repo_info_dict=f16fe1e576e5fb5fdc3c94b320b0d6447be8ac7d:7b2267656e657269635f7574696c73223a205b2247656e65726963205574696c73222c2022687474703a2f2f64736f6272616c406d6e656d6f73796e652f7265706f732f64736f6272616c2f67656e657269635f7574696c73222c2022613432633463303334633236225d7d&includes_tools=True" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" Nothing that helps me much. I have has some problems with permissions in the tmp dir, but I reconfigured it and it still does not work. Daniel On 03/16/2012 11:04 AM, Greg Von Kuster wrote:
Hi Daniel,
What does your tool shed paster log say when you get the 404 error trying to install? You can see the paster log by running the following from your Galaxy installation directory when your tool shed is running.
tail -f community_webapp.log
Greg Von Kuster
On Mar 16, 2012, at 4:34 AM, Daniel Sobral wrote:
Hello,
I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool.
In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the tool, it gives me: abort: HTTP Error 404: Not Found .
I can install tools from the main galaxy toolshed without problems. I've also uploaded a test tool to the test toolshed server http://testtoolshed.g2.bx.psu.edu and I could install the tools in my galaxy server.
Any ideas of what I may be doing wrong here with my toolshed server?
From the galaxy Toolshed wiki I cannot see anything to give me a clue about what's going on...
Thanks, Daniel
___________________________________________________________ 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:
Daniel, how about your paster log from your Galaxy instance - what does it tell you? Your logs should tell you what is causing the 404 error. 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" At the Galaxy end, your Galaxy paster log should show something like this: galaxy.util.shed_util DEBUG 2012-03-16 09:48:29,952 Installing repository 'filter' galaxy.util.shed_util DEBUG 2012-03-16 09:48:29,953 Cloning http://test@gvk.bx.psu.edu:9009/repos/test/filter destination directory: filter requesting all changes adding changesets adding manifests adding file changes added 1 changesets with 2 changes to 2 files updating to branch default 2 files updated, 0 files merged, 0 files removed, 0 files unresolved galaxy.util.shed_util DEBUG 2012-03-16 09:48:30,380 Updating cloned repository to revision "8ab8044881c6" 0 files updated, 0 files merged, 0 files removed, 0 files unresolved galaxy.util.shed_util DEBUG 2012-03-16 09:48:30,769 Adding new row (or updating an existing row) for repository 'filter' in the tool_shed_repository table. 128.118.200.161 - - [16/Mar/2012:09:48:29 -0400] "POST /admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Fgvk.bx.psu.edu%3A9009%2F&repo_info_dict=ead5f9bd4541ae835f18747280d80b5790b7d314%3A7b2266696c746572223a205b2266696c746572222c2022687474703a2f2f746573744067766b2e62782e7073752e6564753a393030392f7265706f732f746573742f66696c746572222c2022386162383034343838316336225d7d&includes_tools=True HTTP/1.1" 302 - "http://gvk.bx.psu.edu:8763/admin_toolshed/install_repository?tool_shed_url=http://gvk.bx.psu.edu:9009/&repo_info_dict=ead5f9bd4541ae835f18747280d80b5790b7d314:7b2266696c746572223a205b2266696c746572222c2022687474703a2f2f746573744067766b2e62782e7073752e6564753a393030392f7265706f732f746573742f66696c746572222c2022386162383034343838316336225d7d&includes_tools=True" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.54.16 (KHTML, like Gecko) Version/5.1.4 Safari/534.54.16" 128.118.200.161 - - [16/Mar/2012:09:48:31 -0400] "GET /admin_toolshed/browse_repositories?status=done&message=Installed+1+repository+and+all+tools+were+loaded+into+the+tool+panel+outside+of+any+sections.%3Cbr%2F%3EInstalled+repositories%3A+filter.%3Cbr%2F%3E HTTP/1.1" 200 - "http://gvk.bx.psu.edu:8763/admin_toolshed/install_repository?tool_shed_url=http://gvk.bx.psu.edu:9009/&repo_info_dict=ead5f9bd4541ae835f18747280d80b5790b7d314:7b2266696c746572223a205b2266696c746572222c2022687474703a2f2f746573744067766b2e62782e7073752e6564753a393030392f7265706f732f746573742f66696c746572222c2022386162383034343838316336225d7d&includes_tools=True" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/534.54.16 (KHTML, like Gecko) Version/5.1.4 Safari/534.54.16" On Mar 16, 2012, at 8:32 AM, Daniel Sobral wrote:
Hi Greg,
The paster log from the toolshed server does not tells me much:
172.22.50.249 - - [16/Mar/2012:12:27:31 +0100] "GET /toolshed/repository/preview_tools_in_changeset?repository_id=2bccd98f7ba1e82a&changeset_revision=a42c4c034c26&webapp=galaxy HTTP/1.1" 200 - "http://myserver/toolshed//repository/browse_valid_repositories?galaxy_url=http://myserver/galaxy/&webapp=galaxy" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2" 172.22.50.249 - - [16/Mar/2012:12:27:44 +0100] "GET /toolshed/repository/install_repository_revision?repository_id=2bccd98f7ba1e82a&changeset_revision=a42c4c034c26&webapp=galaxy HTTP/1.1" 302 - "http://myserver/toolshed/repository/preview_tools_in_changeset?repository_id=2bccd98f7ba1e82a&changeset_revision=a42c4c034c26&webapp=galaxy" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
But the galaxy paster indicates a failure: 172.22.50.249 - - [16/Mar/2012:12:28:03 +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 - "http://myserver/galaxy/admin_toolshed/install_repository?tool_shed_url=http://myserver/toolshed/&repo_info_dict=f16fe1e576e5fb5fdc3c94b320b0d6447be8ac7d:7b2267656e657269635f7574696c73223a205b2247656e65726963205574696c73222c2022687474703a2f2f64736f6272616c406d6e656d6f73796e652f7265706f732f64736f6272616c2f67656e657269635f7574696c73222c2022613432633463303334633236225d7d&includes_tools=True" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
Nothing that helps me much. I have has some problems with permissions in the tmp dir, but I reconfigured it and it still does not work.
Daniel
On 03/16/2012 11:04 AM, Greg Von Kuster wrote:
Hi Daniel,
What does your tool shed paster log say when you get the 404 error trying to install? You can see the paster log by running the following from your Galaxy installation directory when your tool shed is running.
tail -f community_webapp.log
Greg Von Kuster
On Mar 16, 2012, at 4:34 AM, Daniel Sobral wrote:
Hello,
I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool.
In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the tool, it gives me: abort: HTTP Error 404: Not Found .
I can install tools from the main galaxy toolshed without problems. I've also uploaded a test tool to the test toolshed server http://testtoolshed.g2.bx.psu.edu and I could install the tools in my galaxy server.
Any ideas of what I may be doing wrong here with my toolshed server?
From the galaxy Toolshed wiki I cannot see anything to give me a clue about what's going on...
Thanks, Daniel
___________________________________________________________ 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:
participants (2)
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Daniel Sobral -
Greg Von Kuster