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? - 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