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.
This section is also relevant to this discussion.
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