On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote:
> On Mon, Aug 12, 2013 at 2:04 PM, Bjoern Gruening
> <bjoern.gruen...@gmail.com> wrote:
> > On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote:
> >> On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening
> >> <bjoern.gruen...@gmail.com> wrote:
> >> > On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote:
> >> >> Hi all,
> >> >>
> >> >> I'm currently trying out installation of tools from the Tool Shed
> >> >> on a secondary Galaxy server (not our production server nor
> >> >> my development setup). This is running galaxy-dist, current
> >> >> latest stable I believe:
> >> >>
> >> >> $ sudo -u galaxy hg heads
> >> >> changeset:   10201:ebe87051fadf
> >> >> tag:         tip
> >> >> parent:      10199:8bf64d933704
> >> >> user:        Dannon Baker <dannonba...@me.com>
> >> >> date:        Tue Jul 02 10:48:31 2013 -0400
> >> >> summary:     Fix two more downgrade invocations to accept the
> >> >> migrate_engine parameter
> >> >>
> >> >> changeset:   10200:fd4113962c32
> >> >> branch:      stable
> >> >> parent:      10198:0a06df7da177
> >> >> user:        Dannon Baker <dannonba...@me.com>
> >> >> date:        Tue Jul 02 10:48:31 2013 -0400
> >> >> summary:     Fix two more downgrade invocations to accept the
> >> >> migrate_engine parameter
> >> >>
> >> >> I'm having some problems, e.g.
> >> >>
> >> >> Tool shed repository 'package_numpy_1_7' tool dependencies
> >> >>
> >> >> Name  Version Type    Status  Error
> >> >> atlas         3.10.1  package         Error   Error installing tool 
> >> >> dependency atlas
> >> >> version 3.10.1: [Errno 2] No such file or directory:
> >> >> u'/opt/galaxy-dist-shed-tools/atlas/3.10.1/iuc/package_atlas_3_10/597c0e54eded/env.sh'
> >> >> lapack        3.4.2   package         Error   Error installing tool 
> >> >> dependency lapack
> >> >> version 3.4.2: [Errno 2] No such file or directory:
> >> >> u'/opt/galaxy-dist-shed-tools/lapack/3.4.2/iuc/package_lapack_3_4/98a7d116c15f/env.sh'
> >> >> numpy         1.7.1   package         Error   Error installing tool 
> >> >> dependency numpy
> >> >> version 1.7.1: Unsupported action type 'template_command' in tool
> >> >> dependency definition.
> >> >>
> >> >> Is this due to to galaxy-dist being too old for Tool Shed tools
> >> >> whose XML installation scripts use action template_command?
> >> >>
> >> >> e.g. 
> >> >> http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7/c75482be1d3a
> >> >
> >> > Yes.
> >>
> >> Is there an easy fix where you could upload an older
> >> version of the installation script before you started
> >> using the new template_command action?
> >
> > Sorry, I do not understand the question. To you mean if I could revert
> > the changes and go back to old bash scripts for the time being?
> 
> Yes, that is what I meant.
> 
> > In theory it should be possible. But the aim of my cheetah template
> > patch was to make it easier to write such if else conditions. And create
> > a save fallback to non-atlas users. The next stable release should be
> > out that week, or?
> 
> 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. 
The numpy package on main under the IUC account was uploaded yesterday.
I do not think any other package is using it, or?

Maybe I should update the repository description to reflect that the
newest version is needed?



> Thanks,
> 
> Peter


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