I wrote a script to compare these files mainly to be able to remove tool's 
sections and add our own, but when used to compare main vs sample I've got 2 
sections and 3 tools that are in main but not in sample. Here is the list:

WARNING: --- cshl_library_information: Section from tool_conf.xml.main is not 
in tool_conf.xml.sample. It will be ignored.
WARNING: --- ngs_mapping: Section from tool_conf.xml.main is not in 
tool_conf.xml.sample. It will be ignored.
WARNING: --- filters/condense_characters.xml: Tool from section textutil is not 
in tool_conf.xml.sample. It will be ignored.
WARNING: --- stats/dna_filtering.xml: Tool from section filter is not in 
tool_conf.xml.sample. It will be ignored.
WARNING: --- data_source/hapmapmart.xml: Tool from section rgdat is not in 
tool_conf.xml.sample. It will be ignored.

A list of tools and sections that are in sample file but not in main:

WARNING: +++ data_source/ucsc_tablebrowser_test.xml: New Tool in section 
getext. It will be added.
WARNING: +++ data_source/microbial_import.xml: New Tool in section getext. It 
will be added.
WARNING: +++ data_source/biomart_test.xml: New Tool in section getext. It will 
be added.
WARNING: +++ data_source/cbi_rice_mart.xml: New Tool in section getext. It will 
be added.
WARNING: +++ data_source/flymine_test.xml: New Tool in section getext. It will 
be added.
WARNING: +++ data_source/metabolicmine.xml: New Tool in section getext. It will 
be added.
WARNING: +++ data_source/wormbase_test.xml: New Tool in section getext. It will 
be added.
WARNING: +++ data_source/epigraph_import_test.xml: New Tool in section getext. 
It will be added.
WARNING: +++ data_source/hbvar.xml: New Tool in section getext. It will be 
added.
WARNING: +++ data_source/genomespace_file_browser_prod.xml: New Tool in section 
getext. It will be added.
WARNING: +++ validation/fix_errors.xml: New Tool in section getext. It will be 
added.
WARNING: +++ data_destination/epigraph_test.xml: New Tool in section send. It 
will be added.
WARNING: +++ stats/dna_filtering.xml: New Tool in section textutil. It will be 
added.
WARNING: +++ new_operations/tables_arithmetic_operations.xml: New Tool in 
section textutil. It will be added.
WARNING: +++ filters/axt_to_concat_fasta.xml: New Tool in section convert. It 
will be added.
WARNING: +++ filters/axt_to_fasta.xml: New Tool in section convert. It will be 
added.
WARNING: +++ filters/axt_to_lav.xml: New Tool in section convert. It will be 
added.
WARNING: +++ filters/lav_to_bed.xml: New Tool in section convert. It will be 
added.
WARNING: +++ filters/wiggle_to_simple.xml: New Tool in section convert. It will 
be added.
WARNING: +++ filters/gtf2bedgraph.xml: New Tool in section convert. It will be 
added.
WARNING: +++ maf/maf_split_by_species.xml: New Tool in section fetchAlign. It 
will be added.
WARNING: +++ regVariation/t_test_two_samples.xml: New Tool in section stats. It 
will be added.
WARNING: +++ regVariation/compute_q_values.xml: New Tool in section stats. It 
will be added.
WARNING: +++ stats/MINE.xml: New Tool in section stats. It will be added.
WARNING: +++ stats/count_gff_features.xml: New Tool in section stats. It will 
be added.
WARNING: +++ dwt: New Section. Please update list of unwanted sections, 
otherwise it will be added.
WARNING: +++ plotting/bar_chart.xml: New Tool in section plots. It will be 
added.
WARNING: +++ visualization/LAJ.xml: New Tool in section plots. It will be added.
WARNING: +++ regVariation/delete_overlapping_indels.xml: New Tool in section 
regVar. It will be added.
WARNING: +++ regVariation/compute_motifs_frequency.xml: New Tool in section 
regVar. It will be added.
WARNING: +++ regVariation/compute_motif_frequencies_for_all_motifs.xml: New 
Tool in section regVar. It will be added.
WARNING: +++ regVariation/categorize_elements_satisfying_criteria.xml: New Tool 
in section regVar. It will be added.
WARNING: +++ regVariation/draw_stacked_barplots.xml: New Tool in section 
regVar. It will be added.
WARNING: +++ hyphy/hyphy_dnds_wrapper.xml: New Tool in section hyphy. It will 
be added.
WARNING: +++ evolution/codingSnps.xml: New Tool in section hyphy. It will be 
added.
WARNING: +++ evolution/add_scores.xml: New Tool in section hyphy. It will be 
added.
WARNING: +++ meme/meme.xml: New Tool in section motifs. It will be added.
WARNING: +++ meme/fimo.xml: New Tool in section motifs. It will be added.

WARNING: +++ ncbi_blast_plus_tools: New Section. Please update list of unwanted 
sections, otherwise it will be added.
WARNING: +++ NGS_QC: New Section. Please update list of unwanted sections, 
otherwise it will be added.
WARNING: +++ solexa_tools: New Section. Please update list of unwanted 
sections, otherwise it will be added.
WARNING: +++ indels/indel_table.xml: New Tool in section indel_analysis. It 
will be added.
WARNING: +++ ngs_rna/tophat_color_wrapper.xml: New Tool in section 
ngs-rna-tools. It will be added.
WARNING: +++ variant_detection: New Section. Please update list of unwanted 
sections, otherwise it will be added.
WARNING: +++ peak_calling/ccat_wrapper.xml: New Tool in section peak_calling. 
It will be added.
WARNING: +++ ngs-simulation: New Section. Please update list of unwanted 
sections, otherwise it will be added.
WARNING: +++ vcf_tools: New Section. Please update list of unwanted sections, 
otherwise it will be added.

Is this correct? Thanks to let me know.
Cheers,
Anne. 

On 27 Mar 2012, at 16:57, Anne Pajon wrote:

> Got it. Thanks!
> 
> On 27 Mar 2012, at 16:53, Greg Von Kuster wrote:
> 
>> We have a buildbot set up that runs our functional tests against various 
>> platforms / environments.  The .sample file used by the buildbot tests 
>> everything.  The tool_conf.xml.main contains a subset of everything that is 
>> tested.
>> 
>> On Mar 27, 2012, at 11:48 AM, Anne Pajon wrote:
>> 
>>> Hi Nate,
>>> 
>>> Thanks but I am still confused... sorry. Why these two files are different 
>>> then? Are you not running the functional tests on all the tools available 
>>> at the public server? 
>>> 
>>> Anne.
>>> 
>>> On 27 Mar 2012, at 16:33, Nate Coraor wrote:
>>> 
>>>> On Mar 27, 2012, at 11:17 AM, Anne Pajon wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> I would like to know which tool_conf.xml to use, and would like to know 
>>>>> the difference between the main and the sample one. I know that the 
>>>>> functional tests are running against the tool_conf.xml.sample but what 
>>>>> tool_conf.xml.main is used for? 
>>>> 
>>>> Hi Anne,
>>>> 
>>>> tool_conf.xml.main is used by the public server (Galaxy Main) at 
>>>> usegalaxy.org.
>>>> 
>>>> --nate
>>>> 
>>>>> 
>>>>> Thanks.
>>>>> Anne.
>>>>> --
>>>>> Anne Pajon, Ph.D.
>>>>> Cancer Research UK - Cambridge Research Institute
>>>>> Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
>>>>> anne.pa...@cancer.org.uk | +44 (0)1223 404 334
>>>>> 
>>>>> 
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>>> --
>>> Anne Pajon, Ph.D.
>>> Cancer Research UK - Cambridge Research Institute
>>> Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
>>> anne.pa...@cancer.org.uk | +44 (0)1223 404 334
>>> 
>>> 
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> 
> --
> Anne Pajon, Ph.D.
> Cancer Research UK - Cambridge Research Institute
> Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
> anne.pa...@cancer.org.uk | +44 (0)1223 404 334
> 
> 
> 
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--
Anne Pajon, Ph.D.
Cancer Research UK - Cambridge Research Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pa...@cancer.org.uk | +44 (0)1223 404 334



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