Hey Greg,
thank you so much for this very quick and detailed answer, as well as a fix for the issue. The observed inconsistencies in the flexbar repo are resolved now.
Kind regards Johannes
On Jan 25, 2013, at 7:46 PM, Greg Von Kuster greg@bx.psu.edu wrote:
Hello Johannes,
I reset all of the metadata on your flexbar repository and I believe it now displays everything correctly. Metadata is now associated with the following changeset revisions:
14:69ddef2ec7d2 - this is the repository tip and contains Flexbar version 2.31
12:4cbf6c6d2f2b - this changeset has metadata associated with it because it contains Flexbar version 2.3
5:0a7a3e7559b4 - this changeset also contains Flexbar version 2.3. Metadata is associated with this changeset because you deleted the Flexbar tool from the following changeset (6:c0c9b43670d0)
The behavior you describe is a result of the way you uploaded the various changes to independent files. When you upload a file, a new mercurial changeset revision is created, and metadata is defined based on a comparison of the parent changeset revision and the new repository tip. The basic rule for setting metadata is if certain components of the parent changeset is not equal to or a subset f the current changeset (the tip in this discussion). This approach works very well in most cases, but not so well in corner case scenarios like this one. Setting metadata on repositories in the tool shed is a very complex process, so getting it perfect in every scenario is difficult. I'm always improving the process though, and I'll attempt to correct the behavior for this scenario.
The workaround that corrects the behavior in this and all other corner-case scenarios is to manually reset all metadata on the repository after all of your uploads are completed. This process inspects the entire changelog instead of just the repository tip and immediate parent changeset.
I just committed changeset revision 8663:982aa4ecc7b5 to the Galaxy central repository that allows repository owners to reset all metadata on their repositories using the Repository Actions popup menu form the Manage repository page in the tool shed. This feature used to be restricted to only Tool Shed administrators.
This change set is currently running on the test Galaxy tool shed and will be available on the main Galaxy tool shed 2 Galaxy releases from now.
Thanks very much for reporting this!
Greg Von Kuster
On Jan 25, 2013, at 10:21 AM, Johannes Röhr wrote:
Recently, I updated the Flexbar tool definition in the Galaxy Tool Shed repository flexbar to work with a new version of the program. I changed the version of the tool definition from 2.3 to 2.31, adjusted requirements and uploaded files. However, the Flexbar tool in the repo still shows the old tool version and requirements, whereas the tool command seems to be updated.
Furthermore, the change log shows that new repository metadata is associated with the latest change set, but bizarrely the initial metadata is now associated with commit 11 instead of 12, which was the last bugfix commit before the update (commit 13). The update took place more than a week ago.
Any suggestions why that is the case? Thanks! ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: