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 :(

Peter
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