[phenixbb] moving user home directories

Stephen Graham scg34 at cam.ac.uk
Fri Nov 5 00:26:34 PDT 2010

Hi Nat,

My 2c:

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.

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.

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.

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

Sorry, that ended up more like $2.


On 4 November 2010 18:16, Nathaniel Echols <nechols at lbl.gov> wrote:
> On Wed, Nov 3, 2010 at 2:00 AM, Randy Read <rjr27 at cam.ac.uk> wrote:
>> Although having a sysadmin change the location of your home directory is unusual, a much more common problem is buying a new computer and copying your home directory from one to the other.  It can be very difficult (e.g. when going from Linux to Mac or the reverse) to get the same absolute path for your home directory.  So hopefully your project migration tool will allow that too.
> Working on it. . . a lot of stuff to clean up before this will behave
> reliably, but it's starting to be functional.  Among other things, I'm
> going back to text files, but with some extra optimizations for speed.
>  I'm also going to make the default file handling more rational along
> the way.
> If anyone has strong feelings about how the project
> management/interfaces in the GUI should (or should not) work, now
> would be an excellent time to make them known.  (Comments can be sent
> to me directly instead of the list.)
> -Nat
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Dr Stephen Graham
1851 Research Fellow
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Addenbrooke's Hospital, Hills Road
Cambridge, CB2 0XY, UK
Phone: +44 1223 762 638

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