On Fri, Sep 20, 2013 at 11:10 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Wed, Sep 18, 2013 at 11:47 AM, Peter Cock <p.j.a.c...@googlemail.com> 
> wrote:
>> On Tue, Aug 27, 2013 at 2:18 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
>>> Peter,
>>>
>>> I also tried running the command that returns error code 64 on the same
>>> system that runs the automated tests, and it downloaded the correct file for
>>> that operating system and architecture. So I'm not sure why it's failing
>>> when run through buildbot, but I'll look into it and get back to you.
>>>
>>> I've added a trello card to track progress on this issue:
>>>
>>> https://trello.com/c/9ERDMc7j/1079-toolshed-investigate-cause-of-shell-commands-failing-through-buildbot-when-they-are-valid-commands
>>>
>>>    --Dave B.
>>
>> Hi Dave,
>>
>> Something seems to have changed again on the Test Tool Shed,
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/4ae1bac976f3
>>
>> Installation errors - no functional tests were run for any tools in
>> this changeset revision
>> Tool dependencies
>> TypeNameVersion
>> blast+ package 2.2.26+
>> Error
>> /bin/sh: 2: [[: not found /bin/sh: 3: [[: not found /bin/sh: 4: [[:
>> not found /bin/sh: 6: [[: not found /bin/sh: 7: [[: not found tar:
>> option requires an argument -- 'f' Try `tar --help' or `tar --usage'
>> for more information.
>>
>> Is the test cluster really missing /bin/sh? Can you check that
>> and post the full installation log please?
>>
>> I really would like to push an update to ncbi_blast_plus to the
>> main Tool Shed with an updated README file (using RST)
>> and the new citation information - plus of course handling the
>> binary dependency via the new package:
>>
>> http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
>> http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
>>
>> Once this is done there is a backlog of updates I want to
>> tackle following our productive BoF meeting at GCC2013:
>> http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyBlast
>>
>> Thanks,
>>
>> Peter
>
> A related bug for Greg (I think), despite this strange no /bin/sh
> error, this repository is not listed on the Test Tool Shed under
> "Latest revision: installation errors".
>
> Regards,
>
> Peter

Aside from the oddities reported via the Test Tool Shed testing,
feedback for the package_blast_plus_2_2_26 dependency has
been positive, so I have just updated the BLAST+ wrappers
on the main Tool Shed to use it (v0.0.20):

http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/70e7dcbf6573

Fingers crossed this works 'in the wild', and that the curious
missing /bin/sh issue on the test machines can be solved.

Regards,

Peter
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