This has been confusing for me also. Perhaps if we had a way to distinguish between 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 > 0.0.5)" > 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. > > Thanks, > Clare > > -- > > 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 > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/ >
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