Hi, Galaxy Developers,
I have what I believe to be a basic question/problem with respect to making modifications to the integrated_tool_panel.xml (and or tool_conf.xml). Our Galaxy deployment does have some custom additions made to these files (I did not make these modifications so I am not 100% certain at this point whether or not the modifications to integrated_tool_panel.xml were manual or propagated from elsewhere) , and everything seems to work alright, although I do have a problem that I am having somewhat of a difficult time resolving. Before ask my question, I wanted to confirm my understanding of the wiki page http://wiki.galaxyproject.org/GalaxyToolPanel. I was hoping that somebody could validate the following statements;
1) The only thing that a human being should really ever change in the file "integrated_tool_panel.xml" is the ordering of the groupings (I believe I read on the developer mailing list that it was acceptable to delete sections from here as well, although I am not attempting to validate this at this time). 2) That for all intensive purposes, the integrated_tool_panel.xml should be generated automatically from the files specified in the "tool_config_file" configuration directive in universe_wsgi.ini. 3) That it is perfectly to acceptable to make manual modifications to XML files supplied in the configuration directive "tool_config_file" in the universe_wsgi.ini, or add any number additional XML files to this list (presumably I wouldn't want to make too many manual changes to the shed_tool_conf.xml file, I'm referring to the other XML files, not this one).
The reason I am asking this question is a fairly simple one; every now and then, it appears that new tools are released when new versions of Galaxy are released (i.e. a slightly different default toolset is offered, and thus tool panel and or tool configuration files are generated when the new version of Galaxy is started, at least if I do a fresh install). It appears to me based on some very basic testing that once a manual modification to the tool_conf.xml is made, that the next time a pull for an update is run and Galaxy is restarted, that these files remain as-is; basically, what appears to be happening is that we are running a new version of Galaxy with what seems to be an out-of-date integrated_tool_panel.xml, at least in terms of the tools that are configured as part of the default install; this, in a nutshell, is the fundamental problem I am currently dealing with.
Here is what I'm thinking is the "correct" way to solve my problem; 1) Since we are manually modifying the tools_conf.xml, It seems to me that we are kind of shooting ourselves in the foot in terms of our ability to delete this file and have Galaxy update it when we do an upgrade . Based on what I know I feel that we should do is take all of our custom tools modifications and put them in a separate file called uofc_custom_tools.xml, and then add that to "tool_config_file" to abstract away our custom tool configurations from the default tool_conf.xml. 2) When we upgrade galaxy, delete the tools_conf.xml, and when galaxy starts, let it replace this file with the default from the current changeset. 3) As long as we didn't need to do any manually reordering of elements in the integrated_tool_panel.xml, just delete the integrated_tool_panel.xml, and allow it to be manually re-generated from tool_conf.xml and uofc_custom_tools.xml.
Does this solution sound reasonable? I would be very grateful on any insight anybody could provide in the best way to address this problem. I wish you a wonderful day.
Dan Sullivan