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



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