Repositories that contain only a tool dependency definition file are a special
kind of repository. The tool dependency is considered an orphan tool
dependency because it is not associated with any tools in the same repository.
This orphan designation is not so important in the tool shed itself, but there
will soon be features on the Galaxy side that will be available for
administering orphan tool dependencies installed into a Galaxy instance. The
orphan designation is different in Galaxy than it is in the tool shed.
The important best practice to use for these special repositories is that the
version of the tool dependency package definition should never change within
the repository because doing so will not allow for corrections to the
definition of the older tool dependency package definition in a previous
changeset revision. This is the main reason that the package version is
included in the repository name. Restricting the repository to a single
package version allows for any number of changeset revision fixes to the
definition file. Since some of the instruction sets for installing and
compiling a dependency package are fairly complex, fixes to them must be
Including a tool dependency package version in the repository name also makes
it easier to locate the specific package definition, although this is a
secondary reason for naming them so.
Let me know if this is not clear, as this is a very important detail.
Greg Von Kuster
On Mar 17, 2013, at 5:22 PM, Björn Grüning wrote:
> Hello all!
> Anyone knows why the tool-dependency-packages have a version number in
> there repository names? I want to create a new one and wondered why I
> have to include the version number, because the hg-revisions can keep
> track of different versions of a dependency, or? Is there any
> best-practise guideline? Should we create one?
> galaxy-iuc mailing list
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