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.
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...
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 tool installs but does not appear in the menu.
Other tools install the menu updates just fine.
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.
My shed tool path:<toolbox tool_path="../shed_tools">
My current version:parent: 12441:dc067a95261dAdded tag release_2014.02.10 for changeset 5e605ed6069fbranch: stable
Could someone point me in the right direction?
Sheldon 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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