[phenixbb] moving user home directories

Mark Brooks mark.x.brooks at gmail.com
Fri Nov 5 14:21:57 PDT 2010

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.



On 5 November 2010 20:49, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Fri, Nov 5, 2010 at 12:26 AM, Stephen Graham <scg34 at cam.ac.uk> 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
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