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.be...@ufz.de, www.ufz.de

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