[sharp-discuss] (no subject)

[Clemens Vonrhein]

--Sr1nOIr3CvdE5hEN
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable

Dear Gabor,

>         The only problem I encountered during testing is the
> peak-picking in log-likelihood gradient maps. It finds several
> peaks, but all peaks lie on the first G-SITE (0.00 A). Since really
> everything else works fine, I suspect it might be a well-hidden bug
> in the source.

Yes, I'm aware of that - and it should be fixed in the next release of
Sushi (3.0.16).
 =20
>         The other issue I would like to discuss is a proper
> multi-user setup.  I run the the program under the name of a
> specialised user and the scripts create the log directory with
> privileges 0755, i.e. the users cannot delete it. The same is true
> for AutoSHARP, which creates all the subdirectories with 0755. If I
> change the wrappers (we try to implement an RSH-based submission
> scheme), the directory is owned by the user, and the SHARP job works
> fine, but when one try to do density modification afterwards, SUSHI
> seems to run the uniqueify script under the specialised user (seems
> to run it before the actual job submission), which then doesn't have
> the privilege to write into the log directory. BDG_umask=3D000, so in
> principle it should work.

I know ... the user switching works fine for any job that runs through
the submission system. Unfortunately (as you found out) some steps are
not done this way - mainly because they involve only VERY short little
scripts and it was thought that it might be an overkill to go through
the whole submission for these.

However, the BDG_umask should take care of that - and produce
directories that are rwx to everyone (if BDG_umask=3D000 is used). I
will have another look at it closely and see if this BDG_umask it not
applied at some point - and will try to fix it in the next release
too.

Sorry about that!

Cheers

Clemens

--=20

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park     Tel: +44-(0)1223-353033
*  Cambridge CB3 0AX, UK           Fax: +44-(0)1223-366889
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************

--Sr1nOIr3CvdE5hEN
Content-Type: application/pgp-signature
Content-Disposition: inline

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.2.1 (GNU/Linux)

iD8DBQE+jDCN4f+nTPEF25QRAheYAJ9QtE9T3DGS816zT+WqmJ0Uaz8igQCfd2gC
IFm4DZTR/tedz3Fh0vMjauk=
=17Ez
-----END PGP SIGNATURE-----

--Sr1nOIr3CvdE5hEN--