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
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 <sloc@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:
participants (2)
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Clare Sloggett -
Ivan Lovric