Hi Sarah,

can you create a reproducible example in a Docker container for me?
Together with a friend I will have a look at this. But we need to short
reproducible example :)

Thanks,
Bjoern


> Dear all,
> 
> I continuously have several issues with tool dependency packages from
> the toolshed and their revisions. It looks like the tools I install
> have requirements for different revisions of the same package_xy
> repository. What I end up with quite often is having the same package
> installed in multiple revisions (see attached
> "galaxytools_multiple_revisions.jpg" screenshot). When I then update
> the older revision, it's still listet twice and additionally the tool
> that had the older one as a dependency now says it's missing a
> repository dependency.
> 
> Although this is already quite annoying and creates a mess within the
> tool list, I could live with it. However, sometimes it completely
> messes up revisions. In the second attached screenshot
> (numpy_revision_issue.jpg) you can see that this numpy repository
> thinks it is revision "300877695495", but it's actual location has
> revision "8b3a5c7061d8". This causes tools that depend on revision
> "300877695495" to think it's there, but when the dependency is
> resolved at runtime of the tool, numpy is not found (since it's
> location is in a different revision's folder) and the run fails. As
> you can also see from the screenshot, resetting the metadata doesn't
> do anything about this. Also reinstalling doesn't work, since the
> database keeps the faulty record and uses it upon reinstallation.
> 
> I think it's a problem that when I install tools that have outdated
> revisions of a package repository as a dependency, they don't
> recognize that a newer version is available (and already installed),
> but instead insist on installing the older revision, too. I don't
> understand why they even have this strict requirement on a specific
> version of a package repo, and not just the version of the tool
> inside.
> 
> Btw. I also noticed that the installation of R packages (e.g. in
> package_dexseq_1_14) silently fails. Some of the requirements and
> also the dexseq R package itself failed the installation, but Galaxy
> didn't recognize any error and it still showed up as "Installed".
> 
> Best regards, Sarah
> 
> 
> ---- Sarah Diehl HPC System Administrator
> 
> UNIVERSITÉ DU LUXEMBOURG
> 
> LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE Campus Belval | Biotech II 
> 6, avenue du Swing L-4371 Belvaux T +352 46 66 44 5360 
> sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>
> http://lcsb.uni.lu<http://lcsb.uni.lu/> ----- This message is
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> 
> 
> 
> 
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