We created a local Galaxy instance in late 2018 by cloning the main public Galaxy and tools were installed using the API. Everything works except that the Tool Pane layout in our Galaxy main page is the outdated version. We really like the layout of the current version of the Tool Pane of the main public Galaxy server, it is very clean and the tool categories (sections) makes a lot of sense. Is there a way to replicate the Tool Pane of the current public main Galaxy server (just the categories and organization would be OK) in our local instance? We understand that it could be done by manually editing the tool_conf.xml file, but just wonder if there is an easy way.
We also love the styles (font, color, etc.) of the current public Galaxy main page, not sure if that could be easily replicated.
Ad 1) The exact ordering and sections of all tools on usegalaxy.org is described in the config file here. You can also have a look on how all usegalaxy.* servers are installing and updating tools via API in an automated manner.
Ad 2) The new tool panel design was rolled out in 19.01 release notes and there is no easy way to replicate that other than updating. Luckily the update procedure should be easy given you have 18.xx version now. See this slide deck
After we restarted our galaxy, we noticed that the tool panel did not change, and the integrated_tool_panel.xml file originated from the public main galaxy was modified
by galaxy.
Then we noticed the following statement in the beginning of the integrated_tool_panel.xml file:
This is Galaxy’s integrated tool panel and should be modified directly only for reordering tools inside a section. Each time Galaxy starts up,this file is synchronized with the various tool config files : tools, sections and labels added to one of
these files, will be added also here in the appropriate place, while elements removed from the tool config files will be correspondingly deleted from this file.
It appears that the sync is the cause where the old looks always come back despite the change of the integrated_tool_panel.xml file.
If you know other steps we should take in order to change the tool panel looks, please kindly let us know.
The integrated_tool_panel file decides the ordering of the sections and the tools within the section, but it has nothing to do with what tools are installed/available in your Galaxy.
In order to replicate both the ordering and contents of the Main’s tool panel in addition to the integrated_tool_panel you also need to install all the tools that Main has in the appropriate sections. The tools installed on Main from the Toolshed are in this file. The recommended way to install this many tools is to use Ephemeris command
There are some other tools on Main defined in the migrated_tools_confhere but those will probably not be relevant to you since they are mostly old.
In addition to what @marten said, you can change the order of sections and tools by modifying integrated_tool_panel.xml but that only works if you change the file when Galaxy is down, otherwise it will be overwritten when Galaxy is stopped/restarted (unless this has changed recently).
Thanks much for your reply, @nsoranzo! Would it be possible to let us know where can we find the integrated_tool_panel.xml for the current usegalaxy.org? The link provided by @marten was NOT the current version.
Since I also would like to restructure and clean the menu of our instance I would like to ask if you succeeded? Maybe you have further tips?
I was wondering if the sections (ids and names) in shed_tool_conf.xml and tool_conf.xml need to be renamed if they are renamed in integrated_tool_panel.xml?