Hi Peter,

I think you need to merge your commits as I cannot seem to transplant
or import the patches properly.

K

On Mon, Apr 4, 2011 at 9:46 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Mon, Apr 4, 2011 at 12:19 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock <p.j.a.c...@googlemail.com> 
>> wrote:
>>> On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock <p.j.a.c...@googlemail.com> 
>>> wrote:
>>>> Hi all,
>>>>
>>>> The NCBI have just released BLAST 2.2.25+ which includes some
>>>> interesting new stuff of interest to the tabular output, ...
>>>
>>> One reason why I want to move to BLAST 2.2.25+ on our local
>>> machine is they fixed the subject IDs in tabular output, ...
>>
>> Hi Kanwei,
>>
>> Could you transplant or merge this commit please?
>> https://bitbucket.org/peterjc/galaxy-central/changeset/ab40f95393ec
>>
>> It updates the test output files to work with BLAST 2.2.25+, which I
>> will be using locally due to several important bug fixes. As you don't
>> offer BLAST+ on the Penn State server I don't expect this to cause
>> you any problems.
>>
>> Also (and unrelated to this change), do you see this from the test suite?
>>
>> $ ./run_functional_tests.sh -id ncbi_blastp_wrapper
>> ...
>> ======================================================================
>> ERROR: NCBI BLAST+ blastp ( ncbi_blastp_wrapper ) > Test-1
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>  File 
>> "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py",
>> line 155, in test_tool
>>    self.do_it( td )
>>  File 
>> "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py",
>> line 71, in do_it
>>    page_inputs =
>> self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs)
>>  File 
>> "/home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py",
>> line 122, in __expand_grouping
>>    elif isinstance(declared_inputs[value.name], str):
>> KeyError: 'blast_type'
>
> Solved, it seems I can't omit any parameters in the <test> and expect
> the defaults to be used. This doesn't seem desirable (new bug?), but the
> quick fix is to add a few lines to the test. Could you commit this too:
>
> https://bitbucket.org/peterjc/galaxy-central/changeset/124e4556f3c5
>
> Thanks,
>
> Peter
>

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