The tool shed forces unique repository names per user account, allowing for 
uniqueness with that combination.  All tools uploaded into a tool shed 
repository are assigned a unique id called a guid, which is unique for all 
tools across all possible tool sheds.  These guids follow a named spacing 
convention that ensures that any tool installed into any Galaxy instance will 
be uniquely identified regardless of "old" tool ids or tool versions.

For example,  the guid for version 0.0.2 of Brad's tool is 

toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/bam_to_bigwig/0.0.2

while the guid for version 0.1 of Lance's tool is 

toolshed.g2.bx.psu.edu/repos/lparsons/bam_to_bigwig/bam_to_bigwig/0.1

This information can be seen when viewing the tool's metadata in the tool shed. 
 When these tools are installed into a local Galaxy instance, this guid is the 
tool's id in Galaxy rather than the "old" id (e.g., tool id="bam_to_bigwig").  
The "old"  id is still important and must be included in the tool config as 
usual, but is not used to identify a tool that is installed in a repository 
from the tool shed.

All of these details are explained in the tool shed wiki in the following 
section.

http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance

This section is also relevant to this discussion.

http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions


On Apr 19, 2012, at 8:55 AM, Peter Cock wrote:

> 
> Galaxy team - why does the ToolShed allow duplicate repository
> names (here bam_to_bigwig) AND duplicate tool IDs (again, here
> bam_to_bigwig)? Won't this cause chaos when sharing workflows?
> I would suggest checking this when a tool is uploaded and rejecting
> repository name or tool ID clashes.
> 
> Regards,
> 
> Peter

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