> 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
> 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 seems to be an out-of-date integrated_tool_panel.xml, at least in terms of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
> Does this solution sound reasonable?
Yes :)! Having local modifications in a separate file makes totally
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.
> Dan Sullivan
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> To search Galaxy mailing lists use the unified search at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: