[galaxy-dev] problems with labels in the tool box and order of the tools

21 Aug 2012

      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")

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")

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.

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")

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?

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