On Wed, Jan 21, 2015 at 6:54 PM, John Chilton <jmchil...@gmail.com> wrote:
> On Wed, Jan 21, 2015 at 10:35 AM, Wolfgang Maier
> <wolfgang.ma...@biologie.uni-freiburg.de> wrote:
>>
>>
>> On 21.01.2015 16:11, John Chilton wrote:
>>>
>>> So the tool dependency stuff didn't change - but the local job runner
>>> now behaves like the other job runners (DRMAA, PBS, etc...) so you
>>> have uncovered a bug for all of them I think. Is this a tool shed tool
>>> or a locally created dependency?
>>>
>>
>> This is a tool shed tool (package_mimodd_0_1_5), but one I uploaded myself
>> (I discovered the bug when I did a test install after updating our local
>> Galaxy).
>>
>>> I need to think about how to solve this more generally but if you want
>>> a quick work around - I think it would work to just replace "python"
>>> in $GALAXY_ROOT/set_metadata.sh with a  hard-coded path to Galaxy's
>>> python or perhaps just "python2".
>>
>>
>> Since I can change the tool shed tool a more "global" solution could be to
>> simply remove the "python" symlink from the python3 virtualenv after its
>> created and have the tool use "python3" explicitly at runtime. I'll try
>> whether that works, but I think it should.
>
> This sounds like a better short-term solution to me - this way older
> versions of Galaxy will still be able to use the recipe. I created a
> Trello issue to track the longer term fix of isolating metadata
> generation from the tool environment - which is needed but could be a
> little disruptive so I would rather push it off until after the next
> release.

Opps - I forgot the link and forgot to cc the mailing list.

https://trello.com/c/aMCwYZsN

-John

>
> Thanks!
>
> -John
>
>>
>>>
>>> Sorry for the inconvenience and thanks for bringing this to our attention.
>>>
>>
>> No problem. I'm glad if I could help with something instead of just asking
>> questions all the time.
>>
>> Wolfgang
>>
>>
>>
>>>
>>> On Tue, Jan 20, 2015 at 12:52 PM, John Chilton <jmchil...@gmail.com>
>>> wrote:
>>>>
>>>> Are you using the local job runner (this will be the case if you
>>>> haven't explicitly configured something like pbs or DRMAA in your
>>>> job_conf.xml file)?
>>>>
>>>> -John
>>>>
>>>> On Tue, Jan 20, 2015 at 12:34 PM, Wolfgang Maier
>>>> <wolfgang.ma...@biologie.uni-freiburg.de> wrote:
>>>>>
>>>>> On 01/20/2015 06:20 PM, Wolfgang Maier wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> I have not seen this error before (I believe not with
>>>>>> latest_2014.10.06)
>>>>>
>>>>>
>>>>>
>>>>> update: confirmed this now. It's enough to hg update to
>>>>> latest_2014.10.06
>>>>> and things are working again.
>>>>>
>>>>> The difference is that when building the dependency shell command the
>>>>> latest
>>>>> release seems to put the call to set_metadata.sh into that command,
>>>>> while
>>>>> before it seems it was run separately.
>>>>>
>>>>>
>>>>> Wolfgang
>>>>>
>>
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