Re: [easybuild] Python packages?

2016-02-09 Thread Pablo Escobar Lopez 
HI Elizabeth,

There are different options to handle python packages in EB. You can use
the "PythonPackage" easyblock or the "Bundle" easyblock. Personally I use
PythonPackage for python apps without extra deps and Bundle for apps with
many deps but this is quite subjective.

Some examples:

https://github.com/hpcugent/easybuild-easyconfigs/blob/242a3e19308754796c7dd800d2f9f6f40f6c9e14/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb
https://github.com/hpcugent/easybuild-easyconfigs/blob/242a3e19308754796c7dd800d2f9f6f40f6c9e14/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.6.eb

https://github.com/hpcugent/easybuild-easyconfigs/blob/242a3e19308754796c7dd800d2f9f6f40f6c9e14/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb
https://github.com/hpcugent/easybuild-easyconfigs/pull/2457

If you want to be able to reproduce your build I recommend you to run EB in
machine without internet access. Many python packages will download extra
dependencies when running "python setup.py build" so to be sure you include
all the deps in the easyconfigs you need to do some try&error in a machine
without internet access so the automatic download fails, then you can check
the error log and add the missing dependencies to the easyconfig

btw, for next easybuild release we will have %(pyver)s and %(pyshorver)s
templates available for the easyconfigs
https://github.com/hpcugent/easybuild-framework/pull/1595

regards,
Pablo.

-- 
Pablo Escobar López
HPC systems engineer
sciCORE, University of Basel
SIB Swiss Institute of Bioinformatics
http://scicore.unibas.ch

2016-02-08 22:50 GMT+01:00 Elizabeth Fischer :

> Hello,
>
> Is there any documentation on how EasyBuild interacts with Python
> packages?  I see there's an EasyBuild for matplotlib, but not for basemap.
> What is the recommended way to go about installing stuff?  Pure EasyBuild?
> EasyBuild + PIP?  EasyBuild + Conda?
>
> I'm really confused...
>
> Thanks,
> -- Elizabeth
>
>


-- 
Pablo Escobar López
HPC systems engineer
sciCORE, University of Basel
SIB Swiss Institute of Bioinformatics
http://scicore.unibas.ch

Re: [easybuild] Python packages?

2016-02-09 Thread Elizabeth Fischer 
...but I'm trying to figure out the model the Python packager uses.
Traditional Python packaging and virtualenv are very different from the
everything-in-its-own-folder approach of EasyBuild.  How does EasyBuild
bridges these two approaches?



On Tue, Feb 9, 2016 at 2:38 AM, Ward Poelmans 
wrote:

> On 08-02-16 22:50, Elizabeth Fischer wrote:
>
> > Is there any documentation on how EasyBuild interacts with Python
> > packages?  I see there's an EasyBuild for matplotlib, but not for
> > basemap.  What is the recommended way to go about installing stuff?
> > Pure EasyBuild?  EasyBuild + PIP?  EasyBuild + Conda?
>
> basemap was added in 2.6? [1].
>
> The method of installing depends on what you want. There is a generic
> pythonpackage easyblock that you can use. But using easy_install/pip/etc
> on top of a EB python install should also work.
>
> Ward
>
> [1] https://github.com/hpcugent/easybuild-easyconfigs/pull/2221
>

Re: [easybuild] Python packages?

2016-02-09 Thread Ward Poelmans 
On 08-02-16 22:50, Elizabeth Fischer wrote:

> Is there any documentation on how EasyBuild interacts with Python
> packages?  I see there's an EasyBuild for matplotlib, but not for
> basemap.  What is the recommended way to go about installing stuff? 
> Pure EasyBuild?  EasyBuild + PIP?  EasyBuild + Conda?

basemap was added in 2.6? [1].

The method of installing depends on what you want. There is a generic
pythonpackage easyblock that you can use. But using easy_install/pip/etc
on top of a EB python install should also work.

Ward

[1] https://github.com/hpcugent/easybuild-easyconfigs/pull/2221

[easybuild] Python packages?

2016-02-08 Thread Elizabeth Fischer 
Hello,

Is there any documentation on how EasyBuild interacts with Python
packages?  I see there's an EasyBuild for matplotlib, but not for basemap.
What is the recommended way to go about installing stuff?  Pure EasyBuild?
EasyBuild + PIP?  EasyBuild + Conda?

I'm really confused...

Thanks,
-- Elizabeth