Hello Hans,

I've committed a fix for this issue in changeset 7560:738b703f725c, which will 
be included in the next Galaxy release.  Thanks for reporting this!

Greg Von Kuster

On Aug 28, 2012, at 5:40 AM, Hans-Rudolf Hotz wrote:

> Hi Greg
> 
> Thank you for your help. Although, "integrated_tool_panel.xml" is 
> re-rewritten after each re-start, I can fix my problem (as you have 
> suggested) by removing it first, and then do a restart.
> 
> Regards,
> Hans
> 
> On 08/27/2012 04:54 PM, Greg Von Kuster wrote:
>> 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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>> 


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