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Question: Succesfully installed tools not shown in tool shed configuration
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gravatar for Coryzaa
11 months ago by
Coryzaa • 10
Coryzaa • 10 wrote:

Hi,

We have been setting-up a Galaxy and whenever we try to install tools from the Galaxy tool shed, they do not appear in the tool list on the interface. Via the admin panel, and on the back-side, we can see that the tools were installed succesfully however it appears that they have never been added to the shed_tool_conf.xml.

Is this default behavior? It seems like something is not going correctly, but I can't figure out what it is.
toolshed installation configuration xml • 502 views
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modified 11 months ago • written 11 months ago by Coryzaa • 10
1
gravatar for Martin Čech
11 months ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

The default behavior is that they are added to the shed_tool_conf.xml. Did you see any errors during the installation?
ADD COMMENT • link written 11 months ago by Martin Čech ♦♦ 4.9k

Thats what I expected.. we did not see any errors during the installation - debug information shows that everything installed correctly..

ADD REPLY • link modified 11 months ago • written 11 months ago by Coryzaa • 10

Can you see them in the integrated_tool_panel.xml? During an installation you can also select a non-default shed_tool_conf to be used - check that and also config in galaxy.ini

ADD REPLY • link written 11 months ago by Martin Čech ♦♦ 4.9k

The integrated_tool_panel.xml is empty, since we have no non-default conf configured we don't have that option - but I wil give it a try tomorrow.

ADD REPLY • link written 11 months ago by Coryzaa • 10
1

It really shouldn't be empty unless you removed all the basic tools (like text manipulation) - did you do that?

ADD REPLY • link written 11 months ago by Martin Čech ♦♦ 4.9k
1

Turned out that the defined tool configuration was not named properly - our ICT department fixed that and that resulted in correctly installed tools.

ADD REPLY • link written 11 months ago by Coryzaa • 10
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