Bugs in Control Panel Element

[mugpeng]

I am trying to design my server's galaxy using galaxy docker from https://github.com/bgruening/docker-galaxy . But I found the change in /etc/galaxy/tool_conf.xml will not according affect the UI on panel.

For example, I edit:

<?xml version='1.0' encoding='utf-8'?>
<toolbox monitor="true">
  <label id="getext_all" text="Get Data Method" />
  <section id="getext" name="Get Data">
    <tool file="data_source/upload.xml" />
  </section>
  <section id="send" name="Send Data">
    <tool file="data_export/send.xml" />
    <tool file="data_export/export_remote.xml" />
  </section>
  <section id="getext_Others" name="Others">
    <tool file="data_source/ucsc_tablebrowser.xml" />
  </section>
</toolbox>

Notice that "Others" is the last section but the UI output is:

Besides, I do not configure built-in Converter but also shows.

Furthermore, I try to add another label to divide plot and data function:

But this time the output is strange again:

These two labels squeeze together.

I try to restart the galaxy docker again, but there is no effect.
I am not sure if this bug relates to #19397

Thank you so much.

Best,
Peng

[bernt-matthias]

What is the value of tool_config_file

galaxy/lib/galaxy/config/sample/galaxy.yml.sample

Line 510 in 9953e07

#tool_config_file: tool_conf.xml

? Maybe you can point me to the used config?

[mugpeng]

I used /etc/galaxy/tool_conf.xml as introduced in https://github.com/bgruening/docker-galaxy?tab=readme-ov-file#Integrating-non-Tool-Shed-tools-into-the-container . I just set as tool_config_file: tool_conf.xml.
Thanks.

[bernt-matthias]

I understand the docs such that you should not modify /etc/galaxy/tool_conf.xml, but create an addition
/local_tools/my_tools.xml. Then set tool_config_file: /etc/galaxy/tool_conf.xml,/local_tools/my_tools.xml in the config.

If you only want to add labels or sections I would even suggest to add another custom tool conf xml file which just defines the labels and the section (in the desired order). The important point here would be to list this one first in the tool_config_file variable.

The display of the converters is controlled by display_builtin_converters here:

galaxy/lib/galaxy/config/sample/galaxy.yml.sample

Line 2955 in 9953e07

#display_builtin_converters: true

[mugpeng]

So it is better to be tool_config_file: /local_tools/my_tools.xml,/etc/galaxy/tool_conf.xml which put the custom file first?