This may take some back-and-forth with you to understand the steps you have
taken so far. Successfully installing a repository that contains tools usually
results in the tools being displayed in the Galaxy tool panel. However, there
may be issues that result in the tools not properly loading. This often occurs
when you stop and restart your Galaxy instance. Your Galaxy pasxter log will
include information about any tool that does not properly load. Uninstalling
and reinstalling the repository will usually not have any affect on this.
On Feb 28, 2014, at 9:17 AM, "Briand, Sheldon" <sheldon.bri...@ssc-spc.gc.ca>
> I’ve been poking around a bit more. It looks as though galaxy isn’t 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
> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
> Sent: Thursday, February 27, 2014 8:18 PM
> To: firstname.lastname@example.org
> Subject: [galaxy-dev] tool trouble
> I’m having trouble with some of my tools not appearing in the Analyze Data
> menu. I’ve 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. I’m 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:dc067a95261d
> Added tag release_2014.02.10 for changeset 5e605ed6069f
> branch: stable
> Could someone point me in the right direction?
> Sheldon Briand
> NRC Research Computing Support Analyst
> Research Computing Support / Soutien Informartique a la Recherche
> Operations, Science Portfolio / Operations, Portefeuil des sciences
> SSC-NRC / SPC-CNRC
> Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> Halifax, NS B3H 3Z1
> 902 426-1677
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To search Galaxy mailing lists use the unified search at: