On Tue, Aug 8, 2017 at 8:01 AM, Matthias Bernt <m.be...@ufz.de> wrote:
> Dear dev-list,
>
> here an answer to my own question.
>
> The problem was that the tool "Group data by a column and perform aggregate
> operation on other columns." returned an error:
>
> Traceback (most recent call last): File
> "/gpfs1/data/galaxy_server/galaxy-dev/tools/stats/grouping.py", line 15, in
> <module> import numpy ImportError: No module named numpy
>
> So I thought that numpy is not installed. But the problem was that for
> running the tool on a cluster the venv needs to be specified in
> job_conf.xml, as documented here:
> https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#galaxy-job-handlers
>
> Two follow up questions:
> - Is it worth to extend the documentation on
> https://galaxyproject.org/admin/config/performance/cluster/ or did I just
> miss something? Does this apply for all remote runners?

I don't know the answer to this - it really feels like a detail Galaxy
should resolve so we can reason about it in a more systematic fashion
since many tools shouldn't be sourcing that activate statement and
Galaxy tracks the tools that should. I thought this should just work
but a lot of documentation points to adding that env line and it
solved your problem in this case.

> - Is it possible to have the <env> tag applied to multiple destinations, eg
> by adding it to the <destinations> instead of to <destination>?

The job conf file can define macros if you want to repeatedly insert
the same XML fragments:

- 
https://github.com/galaxyproject/galaxy/commit/483acd58461217de73a13070797db41cad72dd0d
- https://github.com/galaxyproject/galaxy/pull/362

-John

>
> Cheers,
> Matthias
>
>
>
> On 18.07.2017 17:14, Matthias Bernt wrote:
>>
>> Dear dev-list,
>>
>> again some problems with software in galaxy: I can not get numpy to
>> install.
>>
>> Here is the excerpt from the logs:
>>
>> Successfully downloaded from url:
>> https://depot.galaxyproject.org/software/numpy/numpy_1.9p1_src_all.tar.gz
>>
>> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
>> DEBUG 2017-07-18 17:08:29,264 +
>>                          export
>> PYTHONPATH=$PYTHONPATH:/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python
>> &&
>>                          export ATLAS=$ATLAS_ROOT_PATH &&
>>                          python setup.py install --install-lib
>> /gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python
>> --install-scripts
>> /gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/bin
>>
>>
>> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
>> DEBUG 2017-07-18 17:08:29,384 Writing custom site.cfg for ATLAS in Galaxy
>>
>> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
>> DEBUG 2017-07-18 17:08:29,385 Traceback (most recent call last):
>>
>> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
>> DEBUG 2017-07-18 17:08:29,385   File "setup.py", line 264, in <module>
>>
>> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
>> DEBUG 2017-07-18 17:08:29,385     setup_package()
>>
>> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
>> DEBUG 2017-07-18 17:08:29,385   File "setup.py", line 210, in setup_package
>>
>> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
>> DEBUG 2017-07-18 17:08:29,385     raise RuntimeError("Writing custom
>> site.cfg failed! %s" % ex)
>>
>> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy
>> DEBUG 2017-07-18 17:08:29,385 RuntimeError: Writing custom site.cfg failed!
>> 'ATLAS_LIB_DIR'
>>
>> I need this tool for running: "Group data by a column and perform
>> aggregate operation on other columns." which gives me currently a numpy
>> error:
>>
>> Traceback (most recent call last): File
>> "/gpfs1/data/galaxy_server/galaxy/tools/stats/grouping.py", line 15, in
>> <module> import numpy ImportError: No module named numpy
>>
>> Thanks a lot.
>>
>> Cheers,
>> Matthias
>>
>>
>
> --
>
> -------------------------------------------
> Matthias Bernt
> Bioinformatics Service
> Molekulare Systembiologie (MOLSYB)
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
> Helmholtz Centre for Environmental Research GmbH - UFZ
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> Phone +49 341 235 482296,
> m.be...@ufz.de, www.ufz.de
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