Re: [cctbxbb] Automated Travis CI for phenix

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 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

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wrote:

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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_searchCurrent 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

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