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
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 [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
Sarah DIEHL [sarah.di...@uni.lu]
Sent: Wednesday, October 14, 2015 2:05 PM
Subject: [galaxy-dev] recurring issues with revisions of packages from toolshed
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
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I think it's a problem that when I install tools that have outdated revisions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".
HPC System Administrator
UNIVERSITÉ DU LUXEMBOURG
LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
T +352 46 66 44 5360
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