[galaxy-dev] numpy problem
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
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
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
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Phone +49 341 235 482296,
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Re: [galaxy-dev] Adding a visualization plugin to a galaxy local toolshed
Thanks for your answer, I will look at it. Have a nice day! Sent with [ProtonMail](https://protonmail.com) Secure Email. > Original Message > Subject: Re: [galaxy-dev] Adding a visualization plugin to a galaxy local > toolshed > Local Time: July 18, 2017 9:28 AM > UTC Time: July 18, 2017 7:28 AM > From: bjoern.gruen...@gmail.com > To: Lisa Perus , galaxy-dev@lists.galaxyproject.org > > Hi Lisa, > the Tool Shed does not yet support visualisations. But you can submit > your visualisation directly to the Galaxy codebase. > For example have a look at this PR: > https://github.com/galaxyproject/galaxy/pull/4310 > Hope this helps, > Bjoern > Am 18.07.2017 um 09:21 schrieb Lisa Perus: >> Hi everybody, >> >> I am currently working on a galaxy visualization plugin which I would >> like to share with my colleagues. As it stands, they devised a local >> toolshed where I can upload my tools and which works very well for >> uploading tools with their wrappers. >> >> However, I have no idea how to upload a visualization plugin so that >> they can directly install it from the admin menu. >> >> I tried looking for answers but have not found a solution yet. >> >> Any advice is welcome! >> >> Cheers! >> >> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/ >>___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Re: [galaxy-dev] Adding a visualization plugin to a galaxy local toolshed
Hi Lisa, the Tool Shed does not yet support visualisations. But you can submit your visualisation directly to the Galaxy codebase. For example have a look at this PR: https://github.com/galaxyproject/galaxy/pull/4310 Hope this helps, Bjoern Am 18.07.2017 um 09:21 schrieb Lisa Perus: > Hi everybody, > > I am currently working on a galaxy visualization plugin which I would > like to share with my colleagues. As it stands, they devised a local > toolshed where I can upload my tools and which works very well for > uploading tools with their wrappers. > > However, I have no idea how to upload a visualization plugin so that > they can directly install it from the admin menu. > > I tried looking for answers but have not found a solution yet. > > Any advice is welcome! > > Cheers! > > > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
[galaxy-dev] Adding a visualization plugin to a galaxy local toolshed
Hi everybody, I am currently working on a galaxy visualization plugin which I would like to share with my colleagues. As it stands, they devised a local toolshed where I can upload my tools and which works very well for uploading tools with their wrappers. However, I have no idea how to upload a visualization plugin so that they can directly install it from the admin menu. I tried looking for answers but have not found a solution yet. Any advice is welcome! Cheers!___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
