Hey Peter,

  Thanks for continuing to apply pressure on these issues. I have
pushed some logging into Galaxy's development branch
(https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e9607bbe379d)
that should make that error more informative. I don't know when that
will get pushed out to bitbucket and the shed retested - but once
those two things happen we will hopefully have a better idea what the
problem is (probably some subtle deployment problem - some
incompatible version of samtools on the path? samtools on Galaxy's
path but not the test script's path?).

-John


On Mon, Mar 23, 2015 at 6:06 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <p.j.a.c...@googlemail.com> 
>> wrote:
>>> Hi all,
>>>
>>> I have a query about a failing tool test on the Tool Shed, where it
>>> seems Galaxy is trying to convert both the expected BAM output
>>> and the tool's BAM output into SAM for comparison - but this
>>> fails.
>>>
>>> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>>>
>>> 2015-01-27 02:13:51
>>> ...
>>> Converting local (test-data) bam to sam failed
>>>
>>> (and same error on the second test)
>>
>> https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad is still failing,
>> although now with a more concise traceback:
>>
>> Test runs
>> 2015-01-29 02:26:31
>> Automated test environment
>> Tests that failed
>> Tool id: samtools_depad
>> Tool version: samtools_depad
>> Test: test_tool_000000
>> (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1)
>> Stderr:
>> Traceback:
>> Traceback (most recent call last):
>> ...
>> Converting local (test-data) bam to sam failed
>>
>>> The same occurs on the Test Tool Shed (with a very slightly updated
>>> version of this tool), although with a more concise traceback:
>>>
>>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
>>>
>>> 2015-01-25 08:21:59
>>> ...
>>> Tool id: samtools_depad
>>> Tool version: samtools_depad
>>> Test: test_tool_000000
>>> (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2)
>>> Stderr:
>>> Traceback:
>>> ...
>>> Converting local (test-data) bam to sam failed
>>>
>>
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad also
>> still failing,
>>
>> Test runs
>> 2015-01-25 08:21:59
>> ...
>> Converting local (test-data) bam to sam failed
>
> Still failing on the Test Tool Shed, bug filed on Trello,
> https://trello.com/c/TL0IdLlG/2570-toolshed-converting-local-test-data-bam-to-sam-failed
>
> Tests currently stalled on the main Tool Shed, reported here:
> http://dev.list.galaxyproject.org/Tests-not-being-run-on-toolsheds-tc4666816.html
> https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-March/021708.html
>
> Peter
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