Re: Debian in Sanger (Re: update on binary upload restrictions)
Paul Cager [EMAIL PROTECTED] writes: Tim Cutts wrote: What I'd actually like is some sort of non-root packaging system so that users could build software with decent dependency checking for their shared software infrastructure. Can dpkg be cajoled into doing that? Could you use a schroot instance to do that? You can if you combine it with sbuild (specifically for Debian packaging, though). However, it's still a bit risky, because there are ways the user could abuse their access to the chroot in order to subvert the system (e.g. via the debian/rules binary target or in the postinst of a package pulled in as a build-dependency). Worse, the current design allows the sbuild user unrestricted root access to the chroot. If you don't use schroot, sbuild *requires* unrestricted sudo access to the host system! I do have plans (post-etch) to eliminate the user access to the chroot via sudo or schroot, so that sbuild should become safe for untrusted users. Once I have got my thoughts organised, I'll post them to buildd-tools-devel in the next week. Regards, Roger -- .''`. Roger Leigh : :' : Debian GNU/Linux http://people.debian.org/~rleigh/ `. `' Printing on GNU/Linux? http://gutenprint.sourceforge.net/ `-GPG Public Key: 0x25BFB848 Please GPG sign your mail. pgpw40kCKw0G2.pgp Description: PGP signature
Re: Debian in Sanger (Re: update on binary upload restrictions)
On Thu, Feb 01, 2007 at 10:38:46AM +, Tim Cutts wrote: 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. Does it? I am very interested to hear that Sanger is using Debian on thousands of machines. Do not hesitate to tell us a bit more on [EMAIL PROTECTED] Bioinformatics is part of our effort as we 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 (Oracle, mainly). http://www.oracle.com/technology/tech/linux/install/xe_on_debian.html (dunno whether that's what you need, but Oracle does support their products on Debian these days, if I understand them correctly) -- Lo-lan-do Home is where you have to wash the dishes. -- #debian-devel, Freenode, 2004-09-22 -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
On 6 Feb 2007, at 11:22 am, Wouter Verhelst wrote: http://www.oracle.com/technology/tech/linux/install/xe_on_debian.html (dunno whether that's what you need, but Oracle does support their products on Debian these days, if I understand them correctly) Yes, I know about that (and indeed have given it a whirl), but they don't really support it properly. It's a case of we've made this available for you, but if it doesn't work, tough and that's with the ridiculous uber-expensive support contract we have. Tim -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
On Thu, 1 Feb 2007, Tim Cutts wrote: What I'd actually like is some sort of non-root packaging system so that users could build software with decent dependency checking for their shared software infrastructure. Can dpkg be cajoled into doing that? I've heard about click (or klick) which can be used on Knoppixish live CDs and perhaps something else. Never tested it because I have my personal opinion about such stuff, but perhaps it is worth investigating into this direction. Also LinSpire is doing something like that if I'm not misleaded and I have rumors that they opened the system. Just two vague ideas Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
On Thu, Feb 01, 2007 at 08:10:56PM +, Tim Cutts wrote: What I'd actually like is some sort of non-root packaging system so that users could build software with decent dependency checking for their shared software infrastructure. Can dpkg be cajoled into doing that? I knew people who were doing this with rpm. AFAIK the only tricky part was the pre-seeding of the RPM database with some packages that were installed on the system level (like libc) so the dependency tracking could work. dpkg also has a --root ... option, but unfortunately dpkg seems to check for root privileges before trying to install a package so it is pretty much useless. Gabor -- - MTA SZTAKI Computer and Automation Research Institute Hungarian Academy of Sciences - -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
[Tim Cutts] No. The network admin didn't like the idea of all the mail messages. I think I might just ignore him though. :-) Newer versions of popularity-contest deliver via HTTP, so you should have that worry any more. I see from popcon.debian.org we have 26962 submissions currently. And the rate of increase have not slowed down yet. I guess people are installing a lot of etch machines. :) Friendly, -- Petter Reinholdtsen -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
On 2 Feb 2007, at 10:28 am, Gabor Gombas wrote: On Thu, Feb 01, 2007 at 08:10:56PM +, Tim Cutts wrote: What I'd actually like is some sort of non-root packaging system so that users could build software with decent dependency checking for their shared software infrastructure. Can dpkg be cajoled into doing that? I knew people who were doing this with rpm. AFAIK the only tricky part was the pre-seeding of the RPM database with some packages that were installed on the system level (like libc) so the dependency tracking could work. dpkg also has a --root ... option, but unfortunately dpkg seems to check for root privileges before trying to install a package so it is pretty much useless. Yes, indeed, because --root does a chroot() which requires root privilege. What I'm basically after is a dpkg-alike that uses a different root directory, but without using a chroot, so that non- root users can use it. Tim -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
On Fri, 2 Feb 2007 14:09:59 +, Tim Cutts [EMAIL PROTECTED] said: Yes, indeed, because --root does a chroot() which requires root privilege. What I'm basically after is a dpkg-alike that uses a different root directory, but without using a chroot, so that non- root users can use it. I do this using UML and a copy-on-write fs to play around with. One can have bunches of cow_fs files lying around, for the same root_fs. There was even a script somewhere which set up a structure for per user swap and cow file systems. manoj -- Breast Feeding should not be attempted by fathers with hairy chests, since they can make the baby sneeze and give it wind. -- Mike Harding, The Armchair Anarchist's Almanac Manoj Srivastava [EMAIL PROTECTED] http://www.debian.org/~srivasta/ 1024D/BF24424C print 4966 F272 D093 B493 410B 924B 21BA DABB BF24 424C -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
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. Does it? I am very interested to hear that Sanger is using Debian on thousands of machines. Do not hesitate to tell us a bit more on [EMAIL PROTECTED] Bioinformatics is part of our effort as we 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 (Oracle, mainly). 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 CPUs. 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 cfengine2. 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 alignment programs, and will work on EMBOSS with others soon. http://wiki.debian.org/SequenceAlignment http://alioth.debian.org/projects/pkg-emboss/ 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. Regards, Tim -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
On Thu, 1 Feb 2007, Tim Cutts wrote: [... impresive numbers of Debian usage at Sanger ...] Wow. ;-) 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... It would be great to meet you at DebConf, but would not really like to increase your hope that you will get an official slot. I have heard that the DebConf committee is quite strict, but there is always space for an informal meeting / BOF for interested people. (But I'm doing wild guesses here and perhaps I'm wrong.) In any way I would like to organize a Debian-Med day as we did in 2005 in Helsinki and you are invited to join this. Coordination will happen at debian-med@lists.debian.org mailing list. 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. I do not have the slightest idea about the specific requirements of your users but I wonder, whether a kind of default packaging in a certain version with certain configuration might not be interesting. But that's just an idea. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
On Thursday 01 February 2007 11:38:46 Tim Cutts wrote: On 1 Feb 2007, at 1:00 am, Charles Plessy wrote: I am very interested to hear that Sanger is using Debian on thousands of machines. Do not hesitate to tell us a bit more on [EMAIL PROTECTED] Bioinformatics is part of our effort as we include it in pre-clinical research, and we would love to see our priorities a bit more user-driven. Have you installed the popularity-contest package? 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. Thank you for your insights, Tim. There is probably no point for Debian to compete in the package versions with upstream developers of BioPerl, Wise, EMBOSS and whatever other tools yours and your neighbouring institutes' are providing :o) A main difference of Debian to other Linux distributions is probably the merger of us and you/them, ours and yours/theirs. I am very confident that you will find sponsors external to the Sanger Center of even within who would help in getting your changes into the main distribution. It should be only a few days between submission and its appearance in unstable. Please contact Debian-Med whenever you feel that some action from the side of the Debian commuity could possibly be beneficial for your cause. And somehow I hope that you already feel a part of the community. Best regards Steffen pgpTf6YTROlHb.pgp Description: PGP signature
Re: Debian in Sanger (Re: update on binary upload restrictions)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 1 Feb 2007, at 1:30 pm, Steffen Moeller wrote: Have you installed the popularity-contest package? No. The network admin didn't like the idea of all the mail messages. I think I might just ignore him though. :-) There is probably no point for Debian to compete in the package versions with upstream developers of BioPerl, Wise, EMBOSS and whatever other tools yours and your neighbouring institutes' are providing :o) What I'd actually like is some sort of non-root packaging system so that users could build software with decent dependency checking for their shared software infrastructure. Can dpkg be cajoled into doing that? A main difference of Debian to other Linux distributions is probably the merger of us and you/them, ours and yours/theirs. I am very confident that you will find sponsors external to the Sanger Center of even within who would help in getting your changes into the main distribution. It should be only a few days between submission and its appearance in unstable. Please contact Debian-Med whenever you feel that some action from the side of the Debian commuity could possibly be beneficial for your cause. And somehow I hope that you already feel a part of the community. Thanks. :-) Tim -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.3 (Darwin) iQEVAwUBRcJJWxypeFo2odvPAQLLZwgAwWX7rPWpl2MXlAe3tWwQ2auTFOhq8uru CkOhYVi0uIdjTzxmp3GzKvE3QShkp1hTT4RYvcA4afBqCc0WWxN1LpcuvfW+OFcc iqtWKhIc43cyQNxNVyDk/Nj/Ve0Y9wtNqIBZ0UAV6PMDn2CWwuy2NqHv63E68Kpm iChQqxqiY5JjxrzE5fNJJUZtXpANBEuRRlL7rTNDPOCbCgDUcVpmpp0QkGQ6GrZc 1T/Vw8+BSpJtaPmzYHQlFBjLqz2AyMS5+JITyeYsd44Qv+FlczVez4gd9RQRaoQJ s7yTO3CWFSH7aDiXqYlpYMbwC0zxcdKBDECPx6p+8NjPX/Oq4C5RSA== =wqfE -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
On Thu, 1 Feb 2007, Tim Cutts wrote: On 1 Feb 2007, at 1:30 pm, Steffen Moeller wrote: There is probably no point for Debian to compete in the package versions with upstream developers of BioPerl, Wise, EMBOSS and whatever other tools yours and your neighbouring institutes' are providing :o) What I'd actually like is some sort of non-root packaging system so that users could build software with decent dependency checking for their shared software infrastructure. Can dpkg be cajoled into doing that? About a year ago I was playing with getting emerge to do this. I had gotten to the point where I could emerge most of system and a few other things as a normal user on a debian system and have it install stuff in ~/gentoo/. Most of the changes made it into the portage-prefix branch, but last I checked it was still needing a lot of work. Ivan -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Debian in Sanger (Re: update on binary upload restrictions)
Tim Cutts wrote: What I'd actually like is some sort of non-root packaging system so that users could build software with decent dependency checking for their shared software infrastructure. Can dpkg be cajoled into doing that? Could you use a schroot instance to do that? -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
