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"
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
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
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.
From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:email@example.com] On
Behalf Of Briand, Sheldon
Sent: Thursday, February 27, 2014 8:18 PM
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
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:
My current version:
Added tag release_2014.02.10 for changeset 5e605ed6069f
Could someone point me in the right direction?
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
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