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rlabduke / MolProbity

Protein and nucleic acid validation service
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Flipkin: Add binary command detection for reduce, probe, and prekin. #8

Open jaredsampson opened 7 years ago

jaredsampson commented 7 years ago

For users without a PHENIX installation, hard-coding phenix.xxx paths in the flipkin script (added in 7c39436) is problematic and requires either tinkering with the source or installing an outdated version.

To remedy this, I patched Flipkin to check the shell PATH for standalone and PHENIX-associated executables (e.g. reduce and phenix.reduce) in that order, and use the first one found to execute the program calls. If neither option is found, it now dies with an error asking to please install the program in question.

jaredsampson commented 6 years ago

Hi MolProbity devs - Have you considered incorporating this change (or one like it) to allow flipkin to use standalone (i.e. non-Phenix) versions of reduce, probe, and prekin? In writing the PyMOLProbity plugin (MolProbity-style visualization for PyMOL), I wanted to allow people to use the plugin without installing all of Phenix, so I patched Flipkin and linked to my fork in the installation instructions. It'd be nice to be able to point them to the official distribution instead. Let me know if you have any concerns or suggestions...Perl isn't my native language... @rlabduke @bhintze @chrissciwilliams