What is the configuration setting you are using for the location to install repositories? This is defined by the tool_path attribute of the <toolbox> tag in your shed_tools_conf.xml file. The default is:
On Feb 28, 2014, at 3:47 PM, "Briand, Sheldon" <Sheldon.Briand@SSC-SPC.gc.ca> wrote:Hi,No joy on the migration strategy. Deseq is example of a tool that I installed successfully yesterday.
Do you mean that you installed the deseq repository from the main tool shed:
and that its contained deseq tool "DE Seq (version 1.0.0)" was properly displayed in your Galaxy tool panel? If so, what is now happening?
Bowtie2 is an example of a tool that isnít showing up even though the web interface indicates that it is successfully installed.
Can you uninstall the repsository and reinstall it? If so, what happens?
Hi,Iíve been poking around a bit more. It looks as though galaxy isnít actually downloading and installing the tools. The tool status changes to installed in the web interface and postgres but the tool is not present on disk.What is present on disk? If you install a repository with tools, the repository revision's contents should be on disk. However, if the repository is uninstalled, disk files are deleted. Do you have repositories that are installed but do not have any files on disk?
The log below shows no download and make of the tool and dependancies. Hopefully the log gives a bit more information. Sorry for the second email.tool_shed.util.shed_util_common DEBUG 2014-02-28 09:58:48,567 Updating an existing row for repository 'tophat2' in the tool_shed_repository table, status set to 'New'.tool_shed.util.repository_dependency_util DEBUG 2014-02-28 09:58:48,714 Creating repository dependency objects...The log looks ok at first inspection, but it's not useful without more information.
Hi,Iím having trouble with some of my tools not appearing in the Analyze Data menu. Iíve successfully installed the tools via the manage installed tool shed repositories(so they are installed to disk). I have tried uninstalling and installing again.The above should not be necessary. When you install, are you checking the optional checkboxes to install repository dependencies and tool dependencies? If so, are they installing as well?
The tool installs but does not appear in the menu.Do you have an example of a repository that contains tools that installls corruptly, but the tools do not load into the tool panel?Other tools install the menu updates just fine.Do you have an example of a repsoitory that contains tools that do show up in the tool panel after successfule repository installation?
This is probably due to me corrupting the misbehaving tools installation somehow. Iím guessing that I need to uninstall the tool and wipe some postgres entries.I strongly advise not manually changing inaything in your database suing sql commands. If you have done this, it could be the cause of the behavor you are describing. The Galaxy UI or API should be used.Greg Von Kuster
My shed tool path:<toolbox tool_path="../shed_tools">My current version:parent: 12441:dc067a95261dAdded tag release_2014.02.10 for changeset 5e605ed6069fbranch: stableCould someone point me in the right direction?Thanks,-SheldonSheldon BriandNRC Research Computing Support AnalystResearch Computing Support / Soutien Informartique a la RechercheOperations, Science Portfolio / Operations, Portefeuil des sciencesSSC-NRC / SPC-CNRCRm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue OxfordHalifax, NS B3H 3Z1902 426-1677___________________________________________________________
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