Hi,

also fixed, yes!

Good start in a day, to write positive mails :)
Bjoern

> Hello Bjoern,
> 
> I believe this issue was corrected in changeset 10412:29ab5a6d75a7, which was 
> committed to the stable branch and is running on both tool sheds.  At least I 
> am unable to reproduce the behavior you describe using 3 similar repositories 
> in my local tool shed.  Please let me know if you still encounter this issue.
> 
> Thanks,
> 
> Greg Von Kuster
> 
> 
> On Aug 13, 2013, at 12:49 PM, Bjoern Gruening <bjoern.gruen...@gmail.com> 
> wrote:
> 
> > Hi Dave,
> > 
> > for us I think everything is fixed. But we had a bad bug in the 'single
> > revision' implementation of the new 'Tool dependency definition' type.
> > 
> > We had something like that:
> > 
> > A (tool dependency definition) <- B (tool) <- C (workflow)
> > 
> > We changed A (that was numpy) and thought it would be ok to install the
> > workflow afterwards. Because, if A has only one revision associated than
> > it should be working. But B had a reference to the old revision of A (in
> > the XML file) which causes an error. Or the TS wanted to install two
> > different versions of A. Our fix was to upload B again and than C, to
> > renew the revision tags. That was more a hack than a solution :)
> > 
> > I do not know if that still occurs with the latest version of galaxy, we
> > tested it with the old stable version.
> > 
> > Thanks,
> > Bjoern
> > 
> > 
> > 
> >> Peter, Björn,
> >> 
> >> The August Galaxy release is out, and the template_command is now in the 
> >> stable repository and branch. Regarding matplotlib and numpy, I 
> >> currently only see matplotlib depending on the 74c21f9bdc39 revision of 
> >> numpy. Is this still an issue, or has it been resolved?
> >> 
> >>    --Dave B.
> >> 
> >> On 8/12/13 11:36:00.000, Bjoern Gruening wrote:
> >>> On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote:
> >>>> On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening
> >>>> <bjoern.gruen...@gmail.com> wrote:
> >>>>> On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
> >>>>>> Maybe I should retitle this thread...
> >>>>>> 
> >>>>>> On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock 
> >>>>>> <p.j.a.c...@googlemail.com> wrote:
> >>>>>>> 
> >>>>>>> Thank you - installing the NumPy package now works for me,
> >>>>>>> http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
> >>>>>>> 
> >>>>>>> I'm moving on to something odd with matplotlib instead...
> >>>>>>> 
> >>>>>>> Peter
> >>>>>> 
> >>>>>> There are currently two revisions to the main Tool Shed
> >>>>>> package for numpy,
> >>>>>> http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
> >>>>>> 
> >>>>>> Rev 0: c75482be1d3a - needs not-yet-released features
> >>>>>> Rev 1: 74c21f9bdc39 - simplified
> >>>>>> 
> >>>>>> I'm trying to install a package dependent on this via
> >>>>>> matplotlib - but installing the matplotlib package fails:
> >>>>>> http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2
> >>>>>> 
> >>>>>> This is something odd, why does it think it needs to install
> >>>>>> the rev 0 c75482be1d3a version of package_numpy_1_7?
> >>>>>> See screenshot, except here:
> >>>>>> 
> >>>>>> Repository dependencies - installation of these additional
> >>>>>> repositories is required
> >>>>>> Name  Revision        Owner   Installation status
> >>>>>> package_freetype_2_4  8761091302c4    iuc     Installed
> >>>>>> package_numpy_1_7     74c21f9bdc39    iuc     Installed
> >>>>>> package_numpy_1_7     c75482be1d3a    iuc     Uninstalled
> >>>>>> 
> >>>>>> Yes, the matplotlib tool_dependencies.xml does list the
> >>>>>> original revision:
> >>>>>> 
> >>>>>>     <package name="numpy" version="1.7.1">
> >>>>>>        <repository changeset_revision="c75482be1d3a"
> >>>>>> name="package_numpy_1_7" owner="iuc"
> >>>>>> prior_installation_required="True"
> >>>>>> toolshed="http://toolshed.g2.bx.psu.edu"; />
> >>>>>>     </package>
> >>>>>>     <package name="freetype" version="2.4.11">
> >>>>>>         <repository changeset_revision="8761091302c4"
> >>>>>> name="package_freetype_2_4" owner="iuc"
> >>>>>> prior_installation_required="True"
> >>>>>> toolshed="http://toolshed.g2.bx.psu.edu"; />
> >>>>>>     </package>
> >>>>>> 
> >>>>>> But I thought as a "Tool dependency definition" only the
> >>>>>> tip revision is ever used?
> >>>>> 
> >>>>> That is also what I understood, regardless of the revision there is only
> >>>>> one install able revision. But I guess the TS is generating the path to
> >>>>> numpy from the <package> tag and that points to an old non existing
> >>>>> version.
> >>>> 
> >>>> Hmm. Something for Greg to look at then.
> >>>> 
> >>>>>> After attempting to install this, the status is "Installed, missing
> >>>>>> repository dependencies" and this oddity about wanting two
> >>>>>> revisions of NumPy persists.
> >>>>>> 
> >>>>>> The actual failure appears to be in compiling matplotlib itself...
> >>>>>> I don't think it is finding the NumPy installation.
> >>>>>> 
> >>>>>> Is it possible to view the INSTALLATION.log from within the
> >>>>>> Galaxy Admin web interface?
> >>>>> 
> >>>>> Yes you should see all installed files/folder and the INSTALLATION.log
> >>>>> in your web browser.
> >>>> 
> >>>> Can you give me a little more information on how to see
> >>>> this from within Galaxy?
> >>>> 
> >>>> 1. Open my Galaxy instance and log in,
> >>>> 2. Click on "Admin" from top menu
> >>>> 3. Click on "Manage installed tool shed repositories" on left
> >>>> 4. Select repository of interest
> >>> 
> >>> 5. Click, "Manage tool dependencies"
> >>> 6. Choose one of the dependencies
> >>> 
> >>> There should be a tree like structure to navigate to your
> >>> INSTALLATION.log file besides your env.sh file.
> >>> 
> >>>> At this point the repository drop down menus I see are
> >>>> "Get updates" and "Delete or inactivate". I must be looking
> >>>> in the wrong place?
> >>>> 
> >>>>> 
> >>>>> I can reproduce it here and it fails because of numpy.
> >>>> 
> >>>> OK, that's good - it sounds like the rival revision problem
> >>>> is what is going wrong.
> >>>> 
> >>>>> 
> >>>>> One fix to get it working is to upload again biopython.
> >>>> 
> >>>> Good plan - as discussed here:
> >>>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016001.html
> >>> 
> >>> Done.
> >>> 
> >>>> Thank you,
> >>>> 
> >>>> Peter
> >>> 
> >>> 
> >>> ___________________________________________________________
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> >>> 
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> >>> 
> > 
> > 
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> > 
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> > 
> 



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