On Mon, 2013-08-12 at 14:30 +0100, Peter Cock wrote:
> On Mon, Aug 12, 2013 at 2:18 PM, Bjoern Gruening
> <bjoern.gruen...@gmail.com> wrote:
> > On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote:
> >>
> >> I expect that in the meantime this bug will hit other people
> >> as well (and until the Tool Shed testing is improved I'm a
> >> little worried there could be other 'broken' packages) :(
> >>
> >> If you had a working (minimal non-Altas non-lapack) numpy
> >> tool_dependencies.xml pre-dating the template_command
> >> action it would seem sensible to upload it now to fix the
> >> numpy package on the main Tool Shed.
> >>
> >> I would have thought one of the old revisions from the
> >> numpy package on the Test Tool Shed would work?
> >
> > Yes they do. But if you could not deactivate cpu throttling it will
> > crash and all other dependent packages will not be installed.
> Ah. But at least it would work on some machines, whereas
> right now it will fail on all galaxy-dist installations (until the
> next stable release happens).
> > The numpy package on main under the IUC account was
> > uploaded yesterday. I do not think any other package is
> > using it, or?
> Too late :(
> These repositories on the Main Tool Shed use the numpy
> package directly:
> http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
> http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2
> These all use it via the Biopython package:
> http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer3
> http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
> http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
> These will all use it via the Biopython package when next updated:
> http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
> http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
> There are probably more - Greg can perhaps do a search
> for declared dependencies directly even if this isn't an
> option via the Tool Shed website.
> For these Biopython examples, they don't actually need
> NumPy - so we could perhaps temporarily update the
> Biopython package on the main Tool Shed to install
> without NumPy...
> > Maybe I should update the repository description to reflect that the
> > newest version is needed?
> Updating the description might help - but it doesn't need the
> newest version, it needs the not-yet-released stable version
> of Galaxy :(

Ahhh, right the revisions are gone. So the latest is always the one that
are used. Oh oh ... I will screen through my github history and try to
revert the numpy package until next stable is out.

Oh that was a bad move from me.

> Peter

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