I guess that the conda recipe should be updated to also specify
- python >=3
in the requirements.
On 03/11/16 21:04, Wolfgang Maier wrote:
I'm not quite sure if I understand you correctly, but let's
The original tool wrapper stated
as a dependency. This did not work with at runtime installation at all
because conda cannot resolve python3 and the requirement got ignored
by Galaxy. I changed the requirement tag now to:
and now Galaxy happily installs a __python(a)3.4 environment, but then
it tries to set up a *new* environment for my package, which is still
based on python2.7 and fails as before.
On the bioconda side, all the recipe does is to declare that it
shouldn't be built under python2 using
skip: True # [py2k] in the build section of the recipe.
On 03.11.2016 21:36, Björn Grüning wrote:
> can you check the package? The package should have a dependency on
> python3, if not the package seems to be broken :(
> Am 03.11.2016 um 21:32 schrieb Wolfgang Maier:
>> Hi Björn,
>> Hmm, I guess I should have phrased my question more clearly. What I'm
>> trying to do is to get Galaxy to satisfy a missing tool dependency at
>> *tool runtime* using a bioconda package that is only available for
>> Python3. I am able to satisfy the dependency *manually* by running:
>> conda create --name __<package>@<package_version>
>> <package>==<package_version python=3.5 -c bioconda
>> (following the example at
>> but when I let *Galaxy autoinstall* the package it will use python2.7
>> for the environment, then fail with:
>> Error: Unsatisfiable package specifications.
>> and a hint that <package> conflicts with python 2.7. So my question is:
>> is there any way to inform Galaxy that the dependency requires a conda
>> environment based on python3?
>> On 28.10.2016 19:14, Björn Grüning wrote:
>>> Hi Wolfgang,
>>> can you describe step by step what you are trying to do?
>>> A conda package ships it's own python version, you can see this in the
>>> build-string py35_0 for example. So conda can handle all python
>>> independent of the python version of miniconda.
>>>> Dear all,
>>>> I'm still pretty new to conda tool dependencies management and
>>>> there is
>>>> one thing I cannot find documented anywhere:
>>>> How can I let conda manage tool dependencies that involve python3?
>>>> If I let Galaxy install conda for me, it creates an environment with
>>>> python2, then if there is a tool dependency that has a conda package
>>>> built for only python3 I'm getting an error because of a conflict
>>>> between that package and python2 (not surprisingly), but AFAIU conda
>>>> environments are bound to one particular version of python (or is
>>>> Thanks for any help with this and best wishes,
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