Note these are personal views of another admin not official Galaxy views.
The version issues is a hard one to solve, as automatically updating upstream project is also dangerous as that leaves them in a state that has not be verified by the developer.

Best solution could be for the toolshed to warn if a tool upload would pull in multiple versions.

As for the R install issue.
1. I too find it extremely frustrating how often Galaxy just silently fails.

2. It could be due to a missing R package.
The galaxy tool to determine required R packages appears to miss ones only listed as linked in.
For example I had one which depends on lme4.
This failed to build because RcppEigen was missing
Yet it RccpEigen is only listed as "LinkingTo:"


From: galaxy-dev [] on behalf of Sarah DIEHL []
Sent: Wednesday, October 14, 2015 2:05 PM
Subject: [galaxy-dev] recurring issues with revisions of packages from toolshed

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I think it's a problem that when I install tools that have outdated revisions of a package repository as a dependency, they don't recognize that a newer version is available (and already installed), but instead insist on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 Diehl
HPC System Administrator
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
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