devteam dropped support for installing tool dependencies from toolshed?

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devteam dropped support for installing tool dependencies from toolshed?

Peter Briggs
Dear developers

It looks like some updates to 'devteam'-maintained toolshed tools have
dropped support for tool_dependencies.xml (e.g. fastqc, freebayes), so
their dependencies cannot be automatically installed from the toolshed.
Is this correct? I assume that it's part of the move to enforcing conda
dependency resolution.

Best wishes

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: devteam dropped support for installing tool dependencies from toolshed?

Björn Grüning-3
Hi Peter,

Am 15.12.2016 um 11:28 schrieb Peter Briggs:
> Dear developers
>
> It looks like some updates to 'devteam'-maintained toolshed tools have
> dropped support for tool_dependencies.xml (e.g. fastqc, freebayes), so
> their dependencies cannot be automatically installed from the toolshed.
> Is this correct? I assume that it's part of the move to enforcing conda
> dependency resolution.

Yes. We really hope we are ready to go for conda, John and Marius have
improved the conda support dramatically in the last months.

Thanks,
Bjoern

> Best wishes
>
> Peter
>
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Re: devteam dropped support for installing tool dependencies from toolshed?

Peter Briggs
Hello Bjoern

Thanks for confirming. Is it right that conda dependency resolution is
not supported pre Galaxy v16.01?

Best wishes

Peter

On 15/12/16 10:45, Björn Grüning wrote:

> Hi Peter,
>
> Am 15.12.2016 um 11:28 schrieb Peter Briggs:
>> Dear developers
>>
>> It looks like some updates to 'devteam'-maintained toolshed tools have
>> dropped support for tool_dependencies.xml (e.g. fastqc, freebayes), so
>> their dependencies cannot be automatically installed from the toolshed.
>> Is this correct? I assume that it's part of the move to enforcing conda
>> dependency resolution.
>
> Yes. We really hope we are ready to go for conda, John and Marius have
> improved the conda support dramatically in the last months.
>
> Thanks,
> Bjoern
>
>> Best wishes
>>
>> Peter
>>

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: devteam dropped support for installing tool dependencies from toolshed?

Björn Grüning-3
Hi,

Am 15.12.2016 um 12:09 schrieb Peter Briggs:
> Hello Bjoern
>
> Thanks for confirming. Is it right that conda dependency resolution is
> not supported pre Galaxy v16.01?

Yes. 16.01 was the first version that was introducing it.
To make it clear all older tools will still work, and tool_dependencies
will not go away it is just that they are not recommended anymore.

Ciao,
Bjoern

> Best wishes
>
> Peter
>
> On 15/12/16 10:45, Björn Grüning wrote:
>> Hi Peter,
>>
>> Am 15.12.2016 um 11:28 schrieb Peter Briggs:
>>> Dear developers
>>>
>>> It looks like some updates to 'devteam'-maintained toolshed tools have
>>> dropped support for tool_dependencies.xml (e.g. fastqc, freebayes), so
>>> their dependencies cannot be automatically installed from the toolshed.
>>> Is this correct? I assume that it's part of the move to enforcing conda
>>> dependency resolution.
>>
>> Yes. We really hope we are ready to go for conda, John and Marius have
>> improved the conda support dramatically in the last months.
>>
>> Thanks,
>> Bjoern
>>
>>> Best wishes
>>>
>>> Peter
>>>
>
___________________________________________________________
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