Hi Peter,

On Nov 14, 2013, at 11:27 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> On Wed, Nov 13, 2013 at 12:03 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hello Peter,
>> 
>> Yesterday we discovered what Björn has communicated and added it to the
>> Trello card for this issue:
>> 
>> https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1
>> 
>> ...
>> 
>> becomes the following in your renamed tool_dependencies.xml file:
>> 
>> <tool_dependency>
>>    <package name="samtools" version="0.1.9">
>>        <repository name="package_samtools_0_1_19" owner="iic" />
>>    </package>
>> </tool_dependency>
>> 
>> This is all discussed in the following section of the Tool Shed wiki:
>> 
>> http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories
> 
> I believe that is what I did in response to Bjoern's email, shortly
> before seeing your email (but thank you for the detailed reply):
> 
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/93b8db68dde4
> 
> As an aside, I personally I find the tool_dependencies.xml vs
> repository_dependecies.xml split confusing when defining a
> dependency on a third party tool which is provided by another
> Tool Shed repository. I don't understand why this isn't all done
> with repository_dependecies.xml alone.

If tool dependencies were defined in a repository_dependencies.xml file, the 
definition would be more complex than the current approach we are using. 

1)  A "simple repository dependency" defines a relationship between 2 
repositories and does not consider any of the contents of either repository.  
This relationship is defined in a repository_dependencies.xml file.  A good 
xample is the following repository_dependencies.xml file associated with the 
emboss5 repository at:  
http://devt...@testtoolshed.g2.bx.psu.edu/repos/devteam/emboss_5

The relationship is between the emboss5 repository and its required repository 
named emboss_datatypes.

<?xml version="1.0"?>
<repositories description="Emboss 5 requires the Galaxy applicable data formats 
used by Emboss tools.">
    <repository toolshed="http://testtoolshed.g2.bx.psu.edu"; 
name="emboss_datatypes" owner="devteam" changeset_revision="9f36ad2af086" />
</repositories>


2)  A "complex repository dependency" defines a relationship between some of 
the contents of each of 2 repositories ( the relationship is usually between a 
tool (e.g., xml config and script combination) in the dependent repository and 
a tool component (e.g., 3rd party binary) in the required repository.  This 
relationship is defined in a tool_dependencies.xml file.  A good example is the 
following tool_dependencies.xml file in the same emboss5 repository at:
http://devt...@testtoolshed.g2.bx.psu.edu/repos/devteam/emboss_5

<?xml version="1.0"?>
<tool_dependency>
    <package name="emboss" version="5.0.0">
        <repository changeset_revision="9fd501d0f295" 
name="package_emboss_5_0_0" owner="devteam" 
toolshed="http://testtoolshed.g2.bx.psu.edu"; />
    </package>
</tool_dependency>

The above definition defines only a portion of the relationship to the contents 
of the emboss5 repository.  The remaing portion is the contents of the 
<requirements> tag set in the contained tool(s):

<requirements><requirement type="package" 
version="5.0.0">emboss</requirement></requirements>

For each contained tool that has the above <requirement> tag entry, the tool 
will find the binary dependency installed with the required 
package_emboss_5_0_0 repository when the tool is executed.  Since this 
relationship is defined at the "tool" level and not the "repository" leve, it 
is defined in the tool_dependenciews.xml file.

All of this information is explained in the Tool Shed wiki at the following 
pages.

http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Simple_repository_dependencies

http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_repository_dependencies:_tool_dependency_definitions_that_contain_repository_dependency_definitions


> 
>> 
>> Let me know if this doesn't correct this problem.
>> 
> 
> Last night's Test Tool Shed run confirms this does NOT fix the problem,
> which does indeed appear to be in the Galaxy upload tool which has
> an implicit dependency on samtools for indexing BAM files as John
> suggested.

Yes, we're working extensively on the Tool Shed's install and test framework, 
and we'll figure out the best way to handle this issue.

Thanks!

> 
> Regards,
> 
> Peter
> 
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