numpy problem

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numpy problem

Matthias Bernt
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,
[hidden email], 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
-------------------------------------------
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: numpy problem

Matthias Bernt
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
Phone +49 341 235 482296,
[hidden email], 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
-------------------------------------------
___________________________________________________________
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/
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Re: numpy problem

John Chilton-4
On Tue, Aug 8, 2017 at 8:01 AM, Matthias Bernt <[hidden email]> wrote:

> 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?

I don't know the answer to this - it really feels like a detail Galaxy
should resolve so we can reason about it in a more systematic fashion
since many tools shouldn't be sourcing that activate statement and
Galaxy tracks the tools that should. I thought this should just work
but a lot of documentation points to adding that env line and it
solved your problem in this case.

> - Is it possible to have the <env> tag applied to multiple destinations, eg
> by adding it to the <destinations> instead of to <destination>?

The job conf file can define macros if you want to repeatedly insert
the same XML fragments:

- https://github.com/galaxyproject/galaxy/commit/483acd58461217de73a13070797db41cad72dd0d
- https://github.com/galaxyproject/galaxy/pull/362

-John

>
> 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
> Phone +49 341 235 482296,
> [hidden email], 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
> -------------------------------------------
> ___________________________________________________________
> 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/
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