Hi Hans,
Sorry, I missed your information about your using the latest dist release in my
original response. See my inline comments.
On Aug 21, 2012, at 11:18 AM, Hans-Rudolf Hotz wrote:
> HI
>
>
> We have been struggling with this problem since we updated to
> "changeset:6799:40f1816d6857" (March 12, 2012 release). We never had the time
> to figure out whether it was a bug or whether we made a mistake.
> Unfortunately, it now has reached a point where we have a serious problem
> with our production server.
>
>
> I managed to reproduce the error on a new galaxy-dist clone
> "changeset:7404:ec29ce8e27a1" (July 20, 2012 release):
>
>
> I modify the top of "tool_conf.xml" in the following way (ie: adding a
> label):
>
> <?xml version="1.0"?>
> <toolbox>
> <section name="Get Data" id="getext">
> <tool file="data_source/upload.xml"/>
> <label text="external" id="external_data" />
> <tool file="data_source/ucsc_tablebrowser.xml" />
> <tool file="data_source/ucsc_tablebrowser_test.xml" />
> ...
>
> and it works, after restart, I get the label (see attachment "ss2.tiff")
The above change will automatically be made to your integrated_tool_panel.xml,
and this is why the behavior is as expected.
>
>
>
> I add a new tool definition: "load_abi_reads.xml":
>
> <?xml version="1.0"?>
> <toolbox>
> <section name="Get Data" id="getext">
> <tool file="data_source/upload.xml"/>
> <tool file="hrh/load_abi_reads.xml"/>
> <label text="external" id="external_data" />
> <tool file="data_source/ucsc_tablebrowser.xml" />
> <tool file="data_source/ucsc_tablebrowser_test.xml" />
> ...
>
> and it works, after restart, I get the new tool (see attachment "ss3.tiff")
The same comment I made above applies here as well.
>
>
>
> Now, I don't like the label anymore
>
> <toolbox>
> <section name="Get Data" id="getext">
> <tool file="data_source/upload.xml"/>
> <tool file="hrh/load_abi_reads.xml"/>
> <!-- <label text="external" id="external_data" /> -->
> <tool file="data_source/ucsc_tablebrowser.xml" />
> <tool file="data_source/ucsc_tablebrowser_test.xml" />
>
>
> but, after restart, the label is still there.
If you commented this out in tool_conf.xml, it should have been eliminated
automatically from integrated_tool_panel.xml when you restarted your Galaxy
server. The fact that it wasn't may be a bug. I'll take a look at provide a
fix asap if necessary.
>
>
> Even worse, I add a second tool ("load_novaseq_reads.xml") before the
> first added tool
>
> <?xml version="1.0"?>
> <toolbox>
> <section name="Get Data" id="getext">
> <tool file="data_source/upload.xml"/>
> <tool file="hrh/load_novaseq_reads.xml"/>
> <tool file="hrh/load_abi_reads.xml"/>
> <!-- <label text="external" id="external_data" /> -->
> <tool file="data_source/ucsc_tablebrowser.xml" />
> <tool file="data_source/ucsc_tablebrowser_test.xml" />
>
>
> and after restart, the second tool is put below the first added tool
> (and the label is also still there, see attachment "ss4.tiff")
I'll look at this as well and provide a fix asap if necessary.
>
>
> The display in the web browser corresponds to the file
> "integrated_tool_panel.xml", eg:
>
>
> <?xml version="1.0"?>
> <toolbox>
> <section id="getext" name="Get Data" version="">
> <tool id="upload1" />
> <tool id="load_abi_reads" />
> <tool id="load_novaseq_reads" />
> <label id="external_data" text="external" version="" />
> <tool id="ucsc_table_direct1" />
> <tool id="ucsc_table_direct_test1" />
> <tool id="ucsc_table_direct_archaea1" />
>
>
>
>
> What do I need to change, in order to have the same information in the
> "integrated_tool_panel.xml" file as in the "tool_conf.xml" file with
> regard to order of the tools and removal of labels?
If you've not made any manual changes to your integrated_tool_panel.xml file,
just delete it and it will be re-created automatically when you restart your
Galaxy server. The layour of your tool panel will be as defined in your
tool_conf.xml file. This is just a work-around assuming the above two issues
are bugs that need to be fixed.
>
>
>
>
>
> Any help appreciated
>
> Thank you very much
> Regards, Hans
>
>
>
>
>
>
> --
>
>
>
> Hans-Rudolf Hotz, PhD
> Bioinformatics Support
>
> Friedrich Miescher Institute for Biomedical Research
> Maulbeerstrasse 66
> 4058 Basel/Switzerland
>
>
>
> <ss2.tiff><ss3.tiff><ss4.tiff>___________________________________________________________
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