[cctbxbb] Automated Travis CI for phenix

[Billy Poon]

Hi Elliot,

Also, to run those files from the command-line, you would have something
like,

libtbx.python <CCTBX directory>/mmtbx/command_line/fmodel.py <your
command-line arguments>

The libtbx.python will call python with the proper environment to be
cctbx-aware.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org


On Thu, May 24, 2018 at 10:39 AM Oleg Sobolev <osobolev at lbl.gov> wrote:

> Hi Elliot,
>
> phenix.fmodel and phenix.maps scripts are fully available in cctbx:
>
> cctbx_project/mmtbx/command_line/fmodel.py
> cctbx_project/mmtbx/command_line/maps.py
>
> and have zero dependencies from Phenix closed-source repository.
> You can just call them with cctbx-aware python in your software.
>
> Best regards,
> Oleg Sobolev.
>
> On Thu, May 24, 2018 at 3:37 AM, Elliot Nelson <elliot.nelson at dtc.ox.ac.uk
> > wrote:
>
>> Hi
>>
>>
>> I'm looking to run automated integration tests for software, which
>> currently runs from CCTBX, but also calls phenix scripts. These are
>> phenix.fmodel and phenix.maps. Currently I have a docker image which
>> sources CCP4 to get access to CCTBX, but this will not allow me to test
>> stuff reliant on the phenix scripts.
>>
>> As Phenix is not downloadable on command line (CCP4 build can be got
>> through wget command), it is not obvious as the best way to setup up such a
>> docker build on travis CI. I wouldn't want to source a local download of
>> the software as i am unsure of the licesining implications of hosting a
>> copy of the software.
>>
>>
>> Any suggestions would be greatly appreciated?
>>
>>
>> Software (with dockerfile): https://github.com/nelse003/exhaustive_search
>>
>> <https://github.com/nelse003/exhaustive_search>Current docker image:
>> https://hub.docker.com/r/nelse003/ccp4_phenix_docker/
>>
>>
>> Thanks
>>
>>
>> Elliot
>>
>>
>> DPhil Student, Systems Approaches to Biomedical Science
>> <http://www.sabsidc.ox.ac.uk/>
>> Protein Crystallography <http://www.thesgc.org/groupprofile/9489>,
>> Structural Genomics Consortium, NDM,  University of Oxford
>> Oxford Protein Informatics Group <http://opig.stats.ox.ac.uk/>,
>> Department of Statistics, University of Oxford
>>
>>
>> _______________________________________________
>> cctbxbb mailing list
>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>
>>
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>
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