[phenixbb] moving user home directories

Phil Evans pre at mrc-lmb.cam.ac.uk
Wed Nov 3 02:28:18 PDT 2010

This is a problem (and sometimes a pain) for ccp4i, however in that case it is mitigated by two things

(a) files in the project directory (ie most i/o files) don't have a path, just the file name: only files from elsewhere have the absolute path

(b) as you say, they are text files, so easy to batch edit


On 3 Nov 2010, at 09:00, Randy Read wrote:

> Hi Nat,
> 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.
> Regards,
> Randy
> On 2 Nov 2010, at 18:47, Nathaniel Echols wrote:
>> On Tue, Nov 2, 2010 at 11:31 AM, Ben Eisenbraun
>> <bene at hkl.hms.harvard.edu> wrote:
>>> Our local sysadmins moved everyone's home directory from /nfs/home/foo to
>>> /nfs/userdocs/home/foo, and it appears to have broken most people's PHENIX
>>> projects.
>> Uh-oh.  (Doesn't this break CCP4i too?  I took a look at my old grad
>> school data and it looks like everything is using absolute paths there
>> too - although perhaps since they're text files, it's easier to
>> fix...)
>>> Is there a straightforward way to fix this?  Poking around in the
>>> ~/.phenix/project_db.pkl files, I can see the old paths, but I'm not
>>> exactly sure how to rewrite.  My brute force attempt with sed was
>>> unsuccssful.
>> They're technically binary files (Python pickle format), so I doubt
>> sed will do the job.  I can write you a script to rewrite paths, but
>> it's not a trivial problem.  Migrating projects has been on the to-do
>> list for a while and I'm close to getting it working, but I hadn't
>> planned on anyone moving entire home directories like this.  I don't
>> suppose you can beg the sysadmins to add a symlink named /nfs/home?
>> -Nat
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> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
> Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
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