Hi Peter,

I assume you are using a Galaxy instance within your development environment 
when developing new Galaxy tools so that you ultimately ensure your tool is 
functionally correct.  Adding a local tool shed to your development environment 
will help you ensure that certain tool shed related processes (e.g., setting 
tool shed metadata, installing the repository into a local Galaxy, etc) are 
functionally correct.

With regard to proprietary datatypes (these are datatypes that are included in 
a tool shed repository), the process is simple if the datatypes are all 
subclassed from datatypes defined in the Galaxy framework.   The 
emboss_datatypes are an example of this category, where the "type" attribute is 
something like "galaxy.datatypes.data:Text".  You probably don't need to use a 
local tool shed to help in the development of tools that use this kind of 
proprietary datatype.

The more complex category is when the proprietary datatypes subclass from 
proprietary classes defined in a code file in the repository.  In this case, 
the class file's import statement definitions must be fully qualified.  This is 
the category where using a local tool shed as a component of the development 
process may be beneficial as you can ensure the proprietary datatypes class 
file is written in such a way that the installation process into a local Galaxy 
instance is functionally correct.

There is currently no way to define proprietary datatypes_conf.xml files in a 
configuration entry.

Sorry for the long-winded answer - hopefully the context is helpful.

Greg Von Kuster

On Aug 23, 2012, at 10:11 AM, Peter Cock wrote:

> Dear all,
> 
> Until recently I'd not needed to define new datatypes while
> developing tools for Galaxy - instead using (and sometimes
> modifying) existing datatypes in situ. I have been manually
> 'installing' my in-development tools by added their XML
> files to tool_conf.xml - and this has worked fine to date.
> 
> However, I would now like to experiment with defining or
> modifying datatypes which would eventually be defined via
> a datatypes_conf.xml file in a ToolShed entry.
> 
> My impression from reading the latest wiki documentation
> on http://wiki.g2.bx.psu.edu/Tool%20Shed is that I will have
> to install my own local tool shed.
> 
> Is there a simpler alternative? e.g. Can I add the new
> datatypes_conf.xml file(s) to a configuration entry instead?
> 
> Thanks,
> 
> Peter
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