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?
- Is it possible to have the <env> tag applied to multiple destinations,
eg by adding it to the <destinations> instead of to <destination>?
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
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[email protected], www.ufz.de
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