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Imported io-lib, a Staden library
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Re: Imported io-lib, a Staden library
by Andreas Tille
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On Tue, 8 Jul 2008, Charles Plessy wrote:
> io-lib is a library from the Staden package that is also available > independantly. As we have problems handling the whole Staden package, > and as I had a preliminary package hanging around on my hard drive, I > uploaded it to our repository. Thanks. I also had some trouble when I gave staden a try some time ago and that I want to add the remark that we should definitely try to settle down with one copy of io-lib inside Debian (either the separate or the one whic is in the staden tarball). Moreover I want to repeat my preconceive that io-lib is a quite generic name for a very specific think - perhaps upstream (in CC) might think about this again. > Again, I do not plan to push hard on > getting it in Debian before the release. IMHO we are not in a hurry with this. But I want to use this chance to ping our fellow Debian developers at Sanger to consider some cooperation with the internal Debian project that really targets at their application. He, guys please have another look at the project and perhaps visit http://debian-med.alioth.debian.org/tasks/bio.html or if it is rather about development of biological applications http://debian-med.alioth.debian.org/tasks/bio-dev.html Please consider sharing your work with the Debian community and if you think the currently existing stuff is "not good for you" just try it to tweak it into something that is good enough for you (and other people out there). Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Charles Plessy-12
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Le Tue, Jul 08, 2008 at 02:13:05PM +0200, Andreas Tille a écrit :
> > Thanks. I also had some trouble when I gave staden a try some time > ago and that I want to add the remark that we should definitely try to > settle down with one copy of io-lib inside Debian (either the separate > or the one whic is in the staden tarball). Moreover I want to repeat > my preconceive that io-lib is a quite generic name for a very specific > think - perhaps upstream (in CC) might think about this again. Sure, it was just a quick hack to try to build SRF (I thought it would contain executables but it is only a library). I just uploaded it in our repository: http://svn.debian.org/wsvn/debian-med/trunk/packages/srf/trunk/debian/?rev=0&sc=0 http://srf.sourceforge.net/ -- Charles Plessy Debian-Med packaging team, Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by James Bonfield
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Hello Andreas,
I appreciate the problems with io_lib and the Staden Package, I really do! It causes me no end of hassle too. Unfortunately like a lot of things it's the usual fire-fighting scenario and never any time to tidy up. > Thanks. I also had some trouble when I gave staden a try some time > ago and that I want to add the remark that we should definitely try to > settle down with one copy of io-lib inside Debian (either the separate > or the one whic is in the staden tarball). Moreover I want to repeat If you wish to only have one copy io_lib then that's doable. You may wish to change the build system to use dynamic libraries instead or just face that the build of the staden package programs will be statically linked. Ideally I'd like to rewrite the entire staden build system to use something like autoconf (although maybe one of the newer alternatives that isn't such a dogs breakfast when it comes to dynamic libraries). It should be easier now that we no longer support Mac OS9. MS Windows is more mature with better posix style build environments (eg MSYS/MinGW) and the systems we supported that didn't have functioning libtools are now essentially dead. Agreed on the io_lib name too - it's pretty atrocious, but I'm assuming the name was picked (it predates my work on it) as it was originally just an internal part of a larger package and not distributed separately. > Please consider sharing your work with the Debian community and > if you think the currently existing stuff is "not good for you" just > try it to tweak it into something that is good enough for you (and > other people out there). I think someone else was working on packaging up staden for a debian-derived distribution. I'll have a dig through my mailbox to see if I can recall who. James -- James Bonfield (jkb@...) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Andreas Tille
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On Tue, 8 Jul 2008, James Bonfield wrote:
> I appreciate the problems with io_lib and the Staden Package, I really > do! It causes me no end of hassle too. Unfortunately like a lot of > things it's the usual fire-fighting scenario and never any time to > tidy up. ... the usual thing we all suffer from. > If you wish to only have one copy io_lib then that's doable. You may > wish to change the build system to use dynamic libraries instead or > just face that the build of the staden package programs will be > statically linked. Yes, we would like to provide a library package with dynamic library and a development package with static library and headers. > Ideally I'd like to rewrite the entire staden build system to use > something like autoconf (although maybe one of the newer alternatives > that isn't such a dogs breakfast when it comes to dynamic > libraries). Sounds good. I did not made bad experiences with autoconf - but any modern system might do ... > Agreed on the io_lib name too - it's pretty atrocious, but I'm > assuming the name was picked (it predates my work on it) as it was > originally just an internal part of a larger package and not > distributed separately. I guessed that. If I would be in your shoes I would change it rather sooner than later. > I think someone else was working on packaging up staden for a > debian-derived distribution. I'll have a dig through my mailbox to see > if I can recall who. Well, I have mails about this in my mailbox from about one year ago. But Debian Med is NOT a derived distro - it is just that it is a so called "Custom Debian Distribution" which SOUNDS like it would be something else than Debian (which it isn't). If you think of my mails than I have just one more missinterpretation of this stupid name in my logs. So Debian Med is pure Debian - if somebody else was interested in Staden and has done something - we would be interested. Kind regards and thanks for your quick response Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by James Bonfield
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On Tue, Jul 08, 2008 at 04:32:54PM +0200, Andreas Tille wrote:
> >Ideally I'd like to rewrite the entire staden build system to use > >something like autoconf (although maybe one of the newer alternatives > >that isn't such a dogs breakfast when it comes to dynamic > >libraries). > > Sounds good. I did not made bad experiences with autoconf - but > any modern system might do ... It's not really autoconf but libtool that has given me grief - repeatedly. It never quite worked on the Alliant FX/2800 (a somewhat eclectic system I'll admit) and more recent versions even broke on Digital Unix too, rendering the whole point of using autoconf obsolete. Plus it made debugging in-situ a PITA unless you go through a long-winded full install cycler due to it's insistence on replacing all binaries with shell scripts that then run hidden binaries in dot directories. Although having said that the existing build method using static libraries also cause problems. More recently we just noticed that linking a dynamic library against code that uses io_lib (somewhat inadvisably maybe, but it's what a 3rd partly perl module using inline C was doing) fails as autoconf builds the code using -fpic instead of -fPIC; afterall it doesn't need to link it to work in a dynamic library, only a static one. The only way of working past that is to end up adding machine specific parts to autoconf, which negates its whole purpose in life. Maybe I should just give up and embrace the libtool abomination like the rest of the planet! It probably now works properly on the few remaining systems that anyone still supports. > Well, I have mails about this in my mailbox from about one year ago. > But Debian Med is NOT a derived distro - it is just that it is a > so called "Custom Debian Distribution" which SOUNDS like it would > be something else than Debian (which it isn't). Apologies for the confusion. I recall your earlier mails, but I wasn't referring to these in my comment and nor Debian Med. It turns out I was remembering an Ubuntu variant instead, but it'll still be relevant enough. I found the recent mail: http://sourceforge.net/mailarchive/forum.php?thread_name=484FE66F.E57B.00E6.0%40csir.co.za&forum_name=staden-devel James -- James Bonfield (jkb@...) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Andreas Tille
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On Tue, 8 Jul 2008, James Bonfield wrote:
> Maybe I should just give up and embrace the libtool abomination like > the rest of the planet! It probably now works properly on the few > remaining systems that anyone still supports. When I said autoconf when talking about libraries I certainly also meant libtool. I can not commit really large problems (speaking about Linux only and basically i386). > Apologies for the confusion. I recall your earlier mails, but I wasn't > referring to these in my comment and nor Debian Med. It turns out I > was remembering an Ubuntu variant instead, but it'll still be relevant > enough. I found the recent mail: > > http://sourceforge.net/mailarchive/forum.php?thread_name=484FE66F.E57B.00E6.0%40csir.co.za&forum_name=staden-devel Well, one more reason to consolidate build system (and perhaps also the name to use the chance of doing something new) ... Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Tim Cutts
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On 8 Jul 2008, at 4:55 pm, James Bonfield wrote: > On Tue, Jul 08, 2008 at 04:32:54PM +0200, Andreas Tille wrote: >>> Ideally I'd like to rewrite the entire staden build system to use >>> something like autoconf (although maybe one of the newer >>> alternatives >>> that isn't such a dogs breakfast when it comes to dynamic >>> libraries). >> >> Sounds good. I did not made bad experiences with autoconf - but >> any modern system might do ... > > Maybe I should just give up and embrace the libtool abomination like > the rest of the planet! It probably now works properly on the few > remaining systems that anyone still supports. The last time I tried it, it still didn't work well on Tru64. Trying to compile any recent software that needs it on Tru64 is a nightmare (gtk 2.x, for example) Having said that, I think you could probably justifiably drop support for Tru64 now - HP are no longer selling any Alpha hardware, so you can't buy a new Tru64 system, and although it was widespread in the genomics world, my impression is the vast majority of genomics sites that were on Alpha are doing what Sanger are doing and moving to Linux. I think I heard of one that was moving to AIX, poor souls, but that's the only exception I can think of. Tim -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Tim Cutts
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On 8 Jul 2008, at 1:13 pm, Andreas Tille wrote: > IMHO we are not in a hurry with this. But I want to use this chance > to ping our fellow Debian developers at Sanger to consider some > cooperation > with the internal Debian project that really targets at their > application. In principle, I'm more than happy to help out, but as with everything else, my time is limited. I'm responsible for all central software maintenance at Sanger, so it sort of comes under my remit (I maintain our internal Debian package repository, for example) but the contents of that repository are not generally bio packages, they're local backports from lenny, or perl packages built with dh-make-perl to support other applications. The reasons there's no biomed in there are: 1) Frequently, different groups in the Institute want different versions of the same program to be available, which is hard if we use packaged versions. Exonerate (which I see you've already packaged) is a very bad example of this... in Ensembl's internal software directory there are no less than seven different versions of it. Plus, since its author Guy is a user of the system, there are frequently test development versions which appear and disappear. 2) Using packages suddenly makes it my job (as a sysadmin) to update the software on the machines when required. On the other hand, giving each group an NFS-mounted software directory to which they have write access means that individual groups can install and support whichever version they want, whenever they want, and I only have to maintain the development tools they require. > > He, guys please have another look at the project and perhaps visit > > http://debian-med.alioth.debian.org/tasks/bio.html What I can do to help, if not packaging directly, is act as a liaison with the people actually developing the stuff you want. For example, I know the authors of both SSAHA and Artemis quite well. I've been periodically asking Zemin to alter SSAHA2 so that it can be made DFSG- compliant, and he agrees in principle, it's just a case of his group actually finding the time to do it. I'll ping him again about it. Tim -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Andreas Tille
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On Wed, 9 Jul 2008, Tim Cutts wrote:
> In principle, I'm more than happy to help out, but as with everything else, > my time is limited. ... Sure - we talked about this at DebConf last year and I also remember the reasons you mentioned why you are not using packaged versions. It would be stupid if I would try to argue about your workflow at Sanger which has proven to be reasonable. (I'm probably biased but I think that providing software in packages and enabling users to pin on a certain version leads do better reproducable results than local builds.) > What I can do to help, if not packaging directly, is act as a liaison with > the people actually developing the stuff you want. For example, I know the > authors of both SSAHA and Artemis quite well. I've been periodically asking > Zemin to alter SSAHA2 so that it can be made DFSG-compliant, and he agrees in > principle, it's just a case of his group actually finding the time to do it. > I'll ping him again about it. This help would be really appreciated! Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Charles Plessy-12
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Le Wed, Jul 09, 2008 at 07:08:12AM +0100, Tim Cutts a écrit :
> > 1) Frequently, different groups in the Institute want different > versions of the same program to be available, which is hard if we use > packaged versions. Hi all, this is a very good point. Actually, the situation is similar in my workplace: we have servers (that unfortunately run CentOS) on which the minimum is installed, and everybody compiles what he needs. A tremedous improvement to this situation would be to improve apt so that it can call dpkg with its --root option. Then users would be able to install packaged software in their directory with correct handling of the dependancies. Have a nice day, -- Charles Plessy Debian-Med packaging team, Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Tim Cutts
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On 9 Jul 2008, at 7:42 am, Andreas Tille wrote: > On Wed, 9 Jul 2008, Tim Cutts wrote: > >> In principle, I'm more than happy to help out, but as with >> everything else, my time is limited. ... > > Sure - we talked about this at DebConf last year and I also remember > the > reasons you mentioned why you are not using packaged versions. It > would > be stupid if I would try to argue about your workflow at Sanger > which has > proven to be reasonable. (I'm probably biased but I think that > providing > software in packages and enabling users to pin on a certain version > leads > do better reproducable results than local builds.) That only works if users have their own machines. Most of our bioinformatics goes on a couple of very large shared clusters, so pinning doesn't work. I agree with you in principle, which is why I do package stuff when I can (for example, I package some of the perl modules we need, such as AcePerl, because the version required doesn't change much) Tim -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Andreas Tille
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On Wed, 9 Jul 2008, Charles Plessy wrote:
> this is a very good point. Actually, the situation is similar in my > workplace: we have servers (that unfortunately run CentOS) on which the > minimum is installed, and everybody compiles what he needs. A tremedous > improvement to this situation would be to improve apt so that it can > call dpkg with its --root option. Then users would be able to install > packaged software in their directory with correct handling of the > dependancies. I do not know about --root option but when snapshot.debian.net was functional I used this and pinning via /etc/apt/preferences. If you implement some snapshot.debian.net like repository and educate users how to use pinning you can perfectly live with different versions. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by James Bonfield
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On Wed, Jul 09, 2008 at 10:10:09AM +0200, Andreas Tille wrote:
> I do not know about --root option but when snapshot.debian.net was > functional I used this and pinning via /etc/apt/preferences. If you > implement some snapshot.debian.net like repository and educate users At the risk of exploding a holy flame war, this is something RedHat did years ago with rpm and it proved to be very useful at times. It's certainly a feature I've missed with apt. Requiring editing of /etc files doesn't really solve the problem. Normal users who may wish to maintain their own software tree (as is the case with Tim's comments on /software/<package_or_group>/... directories) should ideally be able to just do "apt-get install --root /software/fubar xyzzy". I suspect it's possible by hacking configuration files and using -c, or if all else fails just hacking the source, but making it easy for users to maintain their own private package tree would be one start down the road of encouraging then to package up their own software in .deb files. James -- James Bonfield (jkb@...) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Charles Plessy-12
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Le Wed, Jul 09, 2008 at 09:09:48AM +0100, Tim Cutts a écrit :
> > I package some of the perl modules we need, such as AcePerl Oh, our ITP #468760 :) I have a detailed debian/copyright file, so if you send us your debian/rules and debian/control, we may have a pacakge for free :) We plan to give write access to all DDs to our SVN repository. Once it is done, do not hesitate to dump packages in; we will eventually do the icing needed for proper distribution. Have a nice day. PS for Andreas: the --root option of dpkg allows to install a Debian binary package in another root, for intance one's home directory. -- Charles Plessy Debian-Med packaging team, Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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dpkg --root / klik (Was: Imported io-lib, a Staden library)
by Andreas Tille
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On Wed, 9 Jul 2008, James Bonfield wrote:
> At the risk of exploding a holy flame war, this is something RedHat > did years ago with rpm and it proved to be very useful at times. It's > certainly a feature I've missed with apt. Ahh, OK. I'm not aware that this feature was ever wanted. Is there active resistance against this feature or did just nobody cared to implement it? > Requiring editing of /etc files doesn't really solve the problem. > Normal users who may wish to maintain their own software tree (as is > the case with Tim's comments on /software/<package_or_group>/... > directories) should ideally be able to just do "apt-get install --root > /software/fubar xyzzy". On Wed, 9 Jul 2008, Charles Plessy wrote: > PS for Andreas: the --root option of dpkg allows to install a Debian > binary package in another root, for intance one's home directory. Ah, OK, something like Klik (http://klik.atekon.de/). I'm in no ways a friend of this - but it seems to do what you want. Kind regards Andreas. PS: Perhaps a topic rather for debian-devel than for debian-med ... -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library
by Tim Cutts
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On 9 Jul 2008, at 8:25 am, Charles Plessy wrote: > Le Wed, Jul 09, 2008 at 07:08:12AM +0100, Tim Cutts a écrit : >> >> 1) Frequently, different groups in the Institute want different >> versions of the same program to be available, which is hard if we use >> packaged versions. > > Hi all, > > this is a very good point. Actually, the situation is similar in my > workplace: we have servers (that unfortunately run CentOS) on which > the > minimum is installed, and everybody compiles what he needs. A > tremedous > improvement to this situation would be to improve apt so that it can > call dpkg with its --root option. Then users would be able to install > packaged software in their directory with correct handling of the > dependancies. Even that doesn't work perfectly - as soon as you do dpkg --root you lose dependencies on the system libraries, which could be very important (for example staden will probably have quite a tight dependency on the precise version of tk installed) Tim -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. -- To UNSUBSCRIBE, email to debian-med-REQUEST@... with a subject of "unsubscribe". Trouble? Contact listmaster@... |
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Re: Imported io-lib, a Staden library |
