Hi Dan,
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seems to be an out-of-date integrated_tool_panel.xml, at least in terms of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?
Yes :)! Having local modifications in a separate file makes totally
sense!
Step 2. is not necessary, imho, you can also merge both files
tools_conf.xml and tools_conf.xml.sample if you like.
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.
You too!
Bjoern
Dan Sullivan
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