Peter -

  When you have previously asked about suite_config.xml I grepped
around and I couldn't find any references to it, did some more greps
just now and I still cannot. My best guess is that is not being used
at all - but I am not a tool shed expert.

Wolfgang -

  I am not aware of being able to enforce an ordering of these things.
It would be a nice feature obviously so I have created a Trello card
for the request - https://trello.com/c/lPOkD4BD.

-John

On Wed, Dec 10, 2014 at 6:08 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Thanks Wolfgang,
>
> I think the suite_config.xml file was originally designed a subset of
> the tool_conf.xml file, inserted into it at run time. I think it could hold
> the tools in the desired order - probably with subsections and
> labels too.
>
> However, I suspect this may not be used with the current
> ToolShed setup - let's wait for the USA based Galaxy team to
> explain later today?
>
> Regards,
>
> Peter
>
> On Wed, Dec 10, 2014 at 10:40 AM, Wolfgang Maier
> <wolfgang.ma...@biologie.uni-freiburg.de> wrote:
>> Hi Peter,
>>
>> here's the link to the package:
>>
>> https://testtoolshed.g2.bx.psu.edu/view/wolma/suite_mimodd_0_1_5
>>
>> It is not using a suite_config.xml file (which I hear of for the first
>> time), but contains just a single repository_dependencies.xml file with this
>> content:
>>
>> <?xml version="1.0"?>
>> <repositories description="Metapackage for the installation of the MiModD
>> suite of tools.">
>>      <repository changeset_revision="9be96af2cb36"
>> name="package_mimodd_0_1_5" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="9840b8f26be9" name="mimodd_fileinfo"
>> owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="666266c4e81f"
>> name="mimodd_ngs_run_annotation" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="74993cc4af07" name="mimodd_convert"
>> owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="1ad8b72a9da8" name="mimodd_reheader"
>> owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="31e73b5e7278" name="mimodd_bamsort"
>> owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="2f47755c35da"
>> name="mimodd_read_alignment" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="7330f7e114f4"
>> name="mimodd_variant_calling" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="35215c432ad9"
>> name="mimodd_extract_variants" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="92cdb9130d08"
>> name="mimodd_coverage_stats" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="ed25fb216505"
>> name="mimodd_deletion_prediction" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="3757a4ee201f" name="mimodd_vcf_filter"
>> owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="36c89c8d555b"
>> name="mimodd_annotate_variants" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="818411f0ff39"
>> name="mimodd_snpeff_genomes" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>>      <repository changeset_revision="3204016d5367"
>> name="mimodd_cloudmap_prepare" owner="wolma"
>> toolshed="https://testtoolshed.g2.bx.psu.edu"; />
>> </repositories>
>>
>> and I'd like Galaxy to add the corresponding tools in exactly this order to
>> the Tools bar. Do I need an additional file to specify this order ?
>>
>> Best,
>> Wolfgang
>>
>>
>>
>> On 12/10/2014 11:31 AM, Peter Cock wrote:
>>>
>>> Hi Wolfgang,
>>>
>>> You didn't include the name or a link to your Test Tool Shed packages.
>>> Are you talking about the suite_config.xml file?
>>>
>>> I'm not sure if Galaxy still uses that, no-one answered my earlier
>>> question:
>>>
>>> http://dev.list.galaxyproject.org/Role-of-suite-config-xml-in-current-Tool-Shed-tc4665887.html
>>>
>>> https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-October/020762.html
>>>
>>> e.g.
>>>
>>> https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/suite_config.xml
>>> https://github.com/peterjc/pico_galaxy/issues/5
>>>
>>> Peter
>>>
>>> On Wed, Dec 10, 2014 at 10:18 AM, Wolfgang Maier
>>> <wolfgang.ma...@biologie.uni-freiburg.de> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I'm currently testing a software package we developed for installation
>>>> from
>>>> the testtoolshed. Things seem to work fine mostly, but there is one thing
>>>> I
>>>> don't know how to solve (if it can be solved).
>>>>
>>>> Our package consists of 14 individual tools, which I uploaded as 14
>>>> separate
>>>> repositories together with a repository suite definition that's taking
>>>> care
>>>> of installing all tools.
>>>>
>>>> Now, somewhat naively as it seems, I expected the order of repository
>>>> declarations in the suite definition file to determine the order of the
>>>> tools in the Galaxy Tools Bar, but, instead, they are added in seemingly
>>>> random order.
>>>>
>>>> So I'm looking for a way to predefine the final order of the tools so
>>>> that
>>>> it makes sense for a typical workflow. Any advice how to address this?
>>>>
>>>> Thanks for your help,
>>>> Wolfgang
>>>>
>>>> ___________________________________________________________
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>>>
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>>
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