[cctbxbb] Automated Travis CI for phenix

[Elliot Nelson]

Hi


Thanks. I had suspected this after looking at the fmodel script, but hadn't yet found the maps options. I will change to call those scripts internally.


Thanks


elliot

________________________________
From: cctbxbb-bounces at phenix-online.org <cctbxbb-bounces at phenix-online.org> on behalf of Billy Poon <BKPoon at lbl.gov>
Sent: 24 May 2018 19:00:18
To: cctbx mailing list
Subject: 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 <osobolev at lbl.gov<mailto: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<mailto: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


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