Hi Nat,<div> 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.</div><div><br>
</div><div>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.</div><div><br></div><div>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:</div>
<div> input {</div><div> project_directory = "/Users/brooks/lysozyme"</div><div>}<br>...then set file names by paths relative to that one. That could be useful for migration of existing .def files, for example.</div>
<div><br></div><div>Thanks again for being receptive to ideas.</div><div><br></div><div>Yours,</div><div><br></div><div>Mark</div><div><br></div><div><br></div><div><br><div class="gmail_quote">On 5 November 2010 20:49, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On Fri, Nov 5, 2010 at 12:26 AM, Stephen Graham <<a href="mailto:scg34@cam.ac.uk">scg34@cam.ac.uk</a>> wrote:<br>
> First off, I'm 100% behind the idea of using text files rather than<br>
> pickles...so if anything goes wrong it can be fixed with a judicious<br>
> sed script.<br>
<br>
</div>Agreed.<br>
<div class="im"><br>
> Second, I would suggest using relative paths whenever practical...<br>
> i.e. if object (file/directory) is in the project directory or a<br>
> subdirectory thereof use a relative path, but if it's somewhere else<br>
> on the file tree entirely (i.e /data for images) use an absolute path.<br>
> At this point I think most of the migration issues that have been<br>
> mentioned would vanish.<br>
<br>
</div>This is practical in some situations but not others; for instance, the<br>
.eff files used for each job still need to have the full path for any<br>
input files. The pickled result objects are an even bigger problem -<br>
fixing this would be a long-term project. Doesn't CCP4i store some<br>
intermediate format between the GUI and the actual run script?<br>
<div class="im"><br>
> Third, it would be really great if you could export a collection of<br>
> jobs (including input files, output files and 'control' (phenix)<br>
> files) as a zip-file or tar file that could be re-imported into<br>
> another user's phenix project. The use case is where you give someone<br>
> else in the lab a hand with building or running some phenix jobs so<br>
> you create a new project, run those jobs and send them back the result<br>
> (say the model). For teaching purposes especially it would be much<br>
> better if you could send back the 'jobs' to re-include in their<br>
> project (so that they know how to run the job themselves next time<br>
> rather than bugging you!). On the up side, if job inport/export via a<br>
> tar/zip file worked you wouldn't necessarily need any other project<br>
> migration tool as people could just zip up their phenix project then<br>
> 'unpack' it on the new machine.<br>
<br>
</div>Exporting and importing projects as a compressed archive is relatively<br>
easy; I'm not sure how to make transferring individual jobs this way<br>
work, however. Keeping the directories and job IDs from overlapping<br>
is going to be tough.<br>
<div class="im"><br>
> Fourth, perhaps I'm just used to CCP4i but I'd really like to see the<br>
> job history on the main phenix window rather than hidden in a dialog<br>
> box.<br>
<br>
</div>It's not an unreasonable request, and not the first time I've heard<br>
this. I'm still trying to figure out how to fit everything into the<br>
main window cleanly - maybe tabs, but I worry about it getting too<br>
cluttered. (On the other hand, as we keep adding programs this will<br>
probably happen anyway unless we redesign the layout.) Although it's<br>
also possible to make this a setting in preferences, and let<br>
individual users decide how they want it to look.<br>
<div><div></div><div class="h5"><br>
-Nat<br>
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