Hi, I would like to know how developers of Galaxy instances are keeping track of binaries version. I know how to check for the installed tools and their different revisions numbers, there is also the workflow version tracking that will let you know when something has been updated but how to keep track of the binaries used by wrappers ? Is there something in Galaxy that I am not aware of or are you using external solution ? Regards, Philip
Hi Philippe, All the Galaxy tool definitions ought to have a <version_command> tag which is run immediately before the actual <command> string (on the same cluster etc). That captures version text from the actual binary used for generating a history entry, and is recorded in the job's meta data. Currently this is not cross-checked to any requested version defined via the ToolShed dependencies - many Galaxy instances do not actually use that (e.g. manual install of binaries, or some other way of installing the binaries). I've filed a feature request on this issue: https://trello.com/c/9nz482vx/2352-verify-tool-versions-match-what-was-expec... Is this the kind of thing you were asking about? Peter On Wed, Feb 4, 2015 at 5:05 AM, Philippe Moncuquet <philippe.mcqt@gmail.com> wrote:
Hi,
I would like to know how developers of Galaxy instances are keeping track of binaries version. I know how to check for the installed tools and their different revisions numbers, there is also the workflow version tracking that will let you know when something has been updated but how to keep track of the binaries used by wrappers ? Is there something in Galaxy that I am not aware of or are you using external solution ?
Regards, Philip
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Hi Peter, Thanks for this. I have upvoted the trello card. Philip 2015-02-04 19:50 GMT+11:00 Peter Cock <p.j.a.cock@googlemail.com>:
Hi Philippe,
All the Galaxy tool definitions ought to have a <version_command> tag which is run immediately before the actual <command> string (on the same cluster etc). That captures version text from the actual binary used for generating a history entry, and is recorded in the job's meta data.
Currently this is not cross-checked to any requested version defined via the ToolShed dependencies - many Galaxy instances do not actually use that (e.g. manual install of binaries, or some other way of installing the binaries).
I've filed a feature request on this issue:
https://trello.com/c/9nz482vx/2352-verify-tool-versions-match-what-was-expec...
Is this the kind of thing you were asking about?
Peter
Hi,
I would like to know how developers of Galaxy instances are keeping
binaries version. I know how to check for the installed tools and their different revisions numbers, there is also the workflow version tracking that will let you know when something has been updated but how to keep
On Wed, Feb 4, 2015 at 5:05 AM, Philippe Moncuquet <philippe.mcqt@gmail.com> wrote: track of track
of the binaries used by wrappers ? Is there something in Galaxy that I am not aware of or are you using external solution ?
Regards, Philip
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
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Peter Cock -
Philippe Moncuquet