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 Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------