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?

Thanks,

Peter
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