On Tue, Aug 8, 2017 at 8:01 AM, Matthias Bernt <m.bernt@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#g...

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/483acd58461217de73a13070797db... - 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 Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de

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