Re: Debian in Sanger (Re: update on binary upload restrictions)
On 1 Feb 2007, at 1:00 am, Charles Plessy wrote:
(Sorry for the noise, I reply on the list since Sanger's mail server
thinks I am a spammer.
I am very interested to hear that Sanger is using Debian on
machines. Do not hesitate to tell us a bit more on
email@example.com. Bioinformatics is part of our effort
include it in "pre-clinical research", and we would love to see our
priorities a bit more user-driven.
Well, we basically use Debian everywhere we can; we have a few
machines running other Linux variants where support requires it
Our Top 500 compute cluster runs almost entirely Debian, this
consists of 600 machines. Two are Tru64 Alphaservers, two are SGI
Altix 350's running a horrible old version of Red Hat, and the
remainder are all IBM blade servers running Debian. A total of 1462
All the Debian machines use the HP SFS cluster filesystem (HP's
productized version of Lustre) for sharing data. Job scheduling is
with Platform LSF, and configuration management is with cfengine2
(our own modification of this; the package currently in etch lacks
some features we need).
Of the 700 or so desktop machines in the Institute, about 300 are
running Debian, the rest Windows. There is a possibility we may move
the desktop machines to Ubuntu, but that is not decided yet. Again,
configuration management, in common with the cluster, is through
We maintain our own internal package repository for both home-grown
packages and local modifications of standard debian packages,
backports and whatnot.
We're quite keen to present something about all this at Debconf; I
realise the deadline has passed, but hopefully they'll squeeze us in...
For the moment, I am finishing to improve support of multiple
programs, and will work on EMBOSS with others soon.
Generally, we are not using Debian packaging techniques for
bioinformatics software. The software requirements of the users move
too quickly, so packaged versions are always out of date, and
besides, different users often require different versions, so we just
leave the maintenance of such software packages to the users
themselves, and store them on a central BlueArc NFS server.
That's not to say that your packaging efforts are not valuable; I
think they're extremely valuable, and will help small laboratories
and the like build functional bioinformatics systems very quickly
without requiring large amounts of assistance from dedicated support
staff they probably can't afford.