Issue with "tool_conf.xml is None" despite it being present

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1

Hi,

I’m encountering an issue when starting Galaxy where the following message appears in the logs, even though tool_conf.xml exists:

galaxy.tool_util.toolbox.base DEBUG 2024-12-12 15:40:04,804 [pN:main,p:3023829,tN:MainThread] Tool path for tool configuration /home/user1/galaxy/config/tool_conf.xml is None

Here’s what I did:

  1. Followed the instructions from Get Galaxy to set up Galaxy on my server.

  2. Created galaxy.yml by running cat galaxy/config/galaxy.yml.sample > galaxy/config/galaxy.yml Then I edited it as needed.

  3. Started Galaxy with sh galaxy/run.sh

  4. Later, I wanted to configure tools using tool_conf.xml. So, I stopped Galaxy and created the file using: cat galaxy/config/tool_conf.xml.sample > galaxy/config/tool_conf.xml Then, I edited the file to include the necessary tool configurations.

After restarting Galaxy, the log keeps showing the above message (tool_conf.xml in None).

Could someone help me understand why this is happening and how to resolve it?

Thanks!

2

Welcome, @kmat

We had another question today about problematic tool installs, so the help I would post back to you would be very similar. Would you like to take a look then let us know about any follow up questions you have?

Let’s start there, thanks! :slight_smile:

3

I wasn’t able to fully resolve this issue, but deleting config/integrated_tool_panel.xml allowed the changes I made to config/tool_conf.xml to be applied. The “…is None” message still appears, but I decided to leave it as is for now.

Thank you,

4

Hi @kmat

Ok, if tools are running for you (find the dependencies) and you are happy, we are happy! :slight_smile:

More about the tool panel and different views can be found here → Tool Panel Administration — Galaxy Project 24.2.dev0 documentation