This has been confusing for me also. Perhaps if we had a way to
the two by prefixing the tool version of a wrapper with "w0.0.5" and the
actual tool version with "v1.3.0"?
I think that Galaxy determines the versions of the tools it loads at
startup in lib/galaxy/tools/__init__.py ToolBox::__add_tool_to_tool_panel()
- log.debug( "Loaded tool id: %s, version: %s into tool panel." % ( tool.id,
tool.version ) ) -
Also check out class Tool which is in the same file...probably requires a
bit more code reading to fully understand the underlying
layers in question...
On Tue, Dec 11, 2012 at 6:43 PM, Clare Sloggett <s...@unimelb.edu.au> wrote:
> Hi guys,
> I wasn't sure if I should send this one to galaxy-user. I have just
> confused myself about the versions of tools displayed within Galaxy.
> If I select the TopHat tool, the tool UI says "Tophat for Illumina
> (version 1.5.0)".
> After I have run the job, the step panel in the History window says
> "Info: TopHat v1.4.1"
> If I select the Cufflinks tool, the tool UI says "Cufflinks (version
> After running the job, the step panel says "Info: cufflinks v1.3.0".
> Looking at the xml files, it does look like the version displayed
> before running is the wrapper and the version displayed on the
> resulting dataset is that of the command-line tool.
> <tool id="tophat" name="Tophat for Illumina" version="1.5.0">
> <!-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 -->
> <tool id="cufflinks" name="Cufflinks" version="0.0.5">
> <!-- Wrapper supports Cufflinks versions v1.3.0 and newer -->
> So looking at the XML it's very clear, but from the versions displayed
> in Galaxy I was completely confused, particularly since the two tophat
> version numbers happened to be similar (1.4.1 and 1.5.0). Maybe we
> should change it so that when Galaxy says "version" it is always
> explicit about whether it's "wrapper version" or just "version"?
> It also seems like there's no way for a user to discover the
> command-line tool version without actually running the tool (or is
> there)? Is this because Galaxy itself does not know this information?
> All this came about because I'm trying to specify to users which
> versions of tools my exported Workflow was built with, and I'm not
> sure how to do it without confusing them.
> Clare Sloggett
> Research Fellow / Bioinformatician
> Life Sciences Computation Centre
> Victorian Life Sciences Computation Initiative
> University of Melbourne, Parkville Campus
> 187 Grattan Street, Carlton, Melbourne
> Victoria 3010, Australia
> Ph: 03 903 53357 M: 0414 854 759
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