Re: [phenixbb] moving user home directories

Hi Nat, Thanks for the excellent software. Would it be possible to have each project directory as a variable, much like the CCP4i "directories & projectDir" list allows you to set. Once you have /Users/brooks/lysozyme and set the project directory to /home/brooks/lysozyme, that would work straight away on a linux computer, for example. I don't think you should clone CCP4i, but that aspect is quite powerful. Even in the .def file, instead of listing "/Users/brooks/lysozyme/peak.mtz" explicitly, one could have a setting: input { project_directory = "/Users/brooks/lysozyme" } ...then set file names by paths relative to that one. That could be useful for migration of existing .def files, for example. Thanks again for being receptive to ideas. Yours, Mark On 5 November 2010 20:49, Nathaniel Echols wrote:

On Fri, Nov 5, 2010 at 12:26 AM, Stephen Graham wrote:

...

First off, I'm 100% behind the idea of using text files rather than pickles...so if anything goes wrong it can be fixed with a judicious sed script.

Agreed.

...

Second, I would suggest using relative paths whenever practical... i.e. if object (file/directory) is in the project directory or a subdirectory thereof use a relative path, but if it's somewhere else on the file tree entirely (i.e /data for images) use an absolute path. At this point I think most of the migration issues that have been mentioned would vanish.

This is practical in some situations but not others; for instance, the .eff files used for each job still need to have the full path for any input files. The pickled result objects are an even bigger problem - fixing this would be a long-term project. Doesn't CCP4i store some intermediate format between the GUI and the actual run script?

...

Third, it would be really great if you could export a collection of jobs (including input files, output files and 'control' (phenix) files) as a zip-file or tar file that could be re-imported into another user's phenix project. The use case is where you give someone else in the lab a hand with building or running some phenix jobs so you create a new project, run those jobs and send them back the result (say the model). For teaching purposes especially it would be much better if you could send back the 'jobs' to re-include in their project (so that they know how to run the job themselves next time rather than bugging you!). On the up side, if job inport/export via a tar/zip file worked you wouldn't necessarily need any other project migration tool as people could just zip up their phenix project then 'unpack' it on the new machine.

Exporting and importing projects as a compressed archive is relatively easy; I'm not sure how to make transferring individual jobs this way work, however. Keeping the directories and job IDs from overlapping is going to be tough.

...

Fourth, perhaps I'm just used to CCP4i but I'd really like to see the job history on the main phenix window rather than hidden in a dialog box.

It's not an unreasonable request, and not the first time I've heard this. I'm still trying to figure out how to fit everything into the main window cleanly - maybe tabs, but I worry about it getting too cluttered. (On the other hand, as we keep adding programs this will probably happen anyway unless we redesign the layout.) Although it's also possible to make this a setting in preferences, and let individual users decide how they want it to look.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb