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an out-of-date integrated_tool_panel.xml, at least in terms of the tools that 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
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