Re: Debian Med Bioinformatics Sprint in Lübeck : post-install
Just a hint on Blast+ This is a rewrite of Blast2 with performance improvements and supposed eaiser to use. But binaries and options were changed. There is a small fdscription we made herte: http://drmotifs.genouest.org/2011/02/new-blast-web-form/ Le 2/2/11 10:08 PM, Andreas Tille a écrit : On Wed, Feb 02, 2011 at 06:19:57PM +, Tim Booth wrote: I generally have an aversion to mailing list servers that create a public mail archive with e-mail addresses unobfuscated, but as I see the damage is now done and my address is on there for all to spam I may as well join. Ahh, hmm, I see. I seem to be routine-blinded because using so many public lists (and using heavy spam filtering). Sorry if I tapped hereby on somebodies shoes - turning the recievers into BCC would have helped here. My fault. :-( The page at the moment rather assumes that you already know how to package. It seems our documentation makes some more of this kind of false assumptions ... It also outlines a development process using SVN-buildpackage that nobody actually seems to follow in real life. May be that is a bit to strong. I *personally* do not like svn-buildpackage and I have heard rumors that people had trouble setting it up. I also have heard that people had more success with git-buildpackage and there seems to be a tendency that people are moving from SVN to Git if you look at the big picture (not specifically at the Debian Med project). (I just noticed that when working on the packaging in the train it would have had advantages to use git because it would have enabled me to make more fine grained commits - but that's a rare case.) In general those tools are designed to make your live easy. There is actually no need to use the tools as long as you provide policy conform packages. If you prefer to do manually what the tool can do for you in principle that's perfectly fine. People who finally included those tools in their own workflow and adapted to using it have learned about their advantages over doing things manually and try to propagate this knowledge to simplify the life of beginners but to some extend newcomers have a limited capacity to learn all the new things and need to adapt slowly. That's fine. Also the page needs to say something to non-developers who come looking for software. It's not immediately clear to a newcomer what exactly Debian Med is doing and why there are no direct package downloads on the site. I'm keen on hearing what you or the other newcomers would have expected to read to get a better understanding. The fact that there is nothing to download can be easily explained: It's just Debian and you do not download but apt-get install. What would you consider a proper place to explain this? (The phrase "Pure Blend" does not mean much to the average user). Maybe a short FAQ is appropriate? http://wiki.debian.org/DebianPureBlends ? During the meeting I was editing the T-Coffee package on my laptop as I had a head start over Paolo in terms of software setup and understanding of package building tools. Our main achievement was to review and update all dependencies (T-Coffee has many). TMalign TMalign will be in new at the end of this week (if nothing unexpected will happen. along with BLAST+ enables a key mode of operation in T-Coffee but currently the BLAST+ bit only works with our bio-linux-blast+ package. I'm continuing to work on this. Did you actually found out what BLAST+ is (I remember you were wondering about the difference between blast2 and blast+). Apart from that we compiled the latest upstream (only on Ubuntu Lucid - someone needs to try it on Sid!) and also did a bit of tidying with help from Andreas. Just tell us were the stuff we should test is located (simply commit the packaging stuff to SVN). Paolo should still be the maintainer of this package from now on, unless we scared him off ;-) As I now have a lot more confidence about my understanding of packaging I'll try to help and encourage him (and others) on the list. I'm fine with giving Paolo any helping hand he might need. Excellent news on Mothur after it sat in the SVN for so long due to license ambiguity. This is a very important package to me so maybe a logical one for me to take on as maintainer once it goes in? Just add yourself to the uploaders field, work on the packaging in SVN and ask on the list that somebody of the DDs should upload. Kind regards Andreas. -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4d4a675f.6080...@irisa.fr
Re: Debian Med Bioinformatics Sprint in Lübeck : post-install
Regarding biomaj, I have created a get-orig-source to download source code and rearrange it to create the debian structure, to be used for packaging. We have an issue with our forge that is being fixed, so it cannot be tested for the moment, but it should be ready in the next few days. On our web site, tarball etc... are for install on "any" system, without the file hierarchy,dependencies etc... There is a debian package, but not an official one, it is a "dirty" deb to use installation on systems. Andreas, I'll let you know once our svn issue is fixed. Olivier Le 2/2/11 1:32 PM, Andreas Tille a écrit : Meta-remark: I removed those e-mail addresses where I know people are reading Debian Med list (specifically lea...@debian.org who was interested in the general resume but not in detailed discussion). I would be happy if we could move the discussion to debian-med@lists.debian.org without the long CC list if I could assume that nobody, who is really interested in this topic will miss the information. So in my next mail I'll probably strip the CC list and there is always the archive of the list in case somebody is interested but is afraid of the list. On Wed, Feb 02, 2011 at 09:39:50AM +, Alan R Williams wrote: I intend to have a look at biomaj in more detail once Olivier has published a downloadable tarball. There is a downloadable tar. It's on the biomaj website http://biomaj.genouest.org I think I agreed with Oliver to have a tarball which can be downloaded by a tool (like uscan which parses new versions) rather than only a human beeing which can enter captchas. Oliver, did I missed something or missunderstood you? Kind regards Andreas. -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4d4a6884.8040...@irisa.fr
Re: Debian Med Bioinformatics Sprint in Lübeck : post-install
Hi Olivier, On Thu, Feb 03, 2011 at 09:29:19AM +0100, Olivier Sallou wrote: > Just a hint on Blast+ > > This is a rewrite of Blast2 with performance improvements and supposed > eaiser to use. > But binaries and options were changed. There is a small fdscription we > made herte: http://drmotifs.genouest.org/2011/02/new-blast-web-form/ Thanks for the hint - I added it to our prospective package list. Seems we need ncbi+ first ... Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110203101542.gc9...@an3as.eu
Re: Debian Med Bioinformatics Sprint in Lübeck : post-install
Some answers on BLAST+ and T-Coffee... > > along with BLAST+ > > enables a key mode of operation in T-Coffee but currently the BLAST+ bit > > only works with our bio-linux-blast+ package. I'm continuing to work on > > this. > > Did you actually found out what BLAST+ is (I remember you were wondering > about the difference between blast2 and blast+). I know about BLAST and BLAST+, but what I'm not sure about is the packaging and distribution. I think NCBI distribute BLAST both as a standalone download and as part of the monster NCBI-tools tarball which is already packaged (not in Debian-Med) by Aaron Ucko. But something is missing from that - certainly something needs to be changed to make T-Coffee happy - but I ran out of time looking at this in Lübeck. > > Apart from that we compiled the latest upstream (only on Ubuntu Lucid - > > someone needs to try it on Sid!) and also did a bit of tidying with help > > from Andreas. > > Just tell us were the stuff we should test is located (simply commit the > packaging stuff to SVN). Just to clarify, I meant the upstream of T-Coffee, not BLAST+. I committed everything to SVN before I packed up on Sunday. I can't imagine any reason why it wouldn't suitable for Sid but I don't want to promise it works as I didn't test it. Cheers, TIM -- To Err is human. To Arrr is Pirate! -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/1296728059.3433.1050.camel@barsukas
TM-align & TM-score: Ready for upload except missing manpage for TMscore
Hi, the tm-align package would be ready for upload if somebody would care for a manpage to TMscore. I have not found any good docs which would enable me writing it. The help2man workaround results in a poor manpage without a good usage guideline. Any volunteers? Remark: I was told by Tim Booth and Pablo Di Tomasso (T-Coffee upstream) that TM-align would be a nice prerequisite for T-Coffee. I have no idea in how far TM-score is needed - it just seems to be quite close and is (now) bundled in one archive by upstream. Please give reasonable advise whate to do out of: 1. Droping TMscore from installation because it is not used 2. Providing TMscore without manpage (not so good) 3. Provide a quite poor manpage using help2man Further remark to the T-Coffee people: Please verify that the spelling of the binary is correct (it is /usr/bin/TMalign and /usr/bin/TMscore). Once this issue is solved I would upload the package. Kind regards Andreas. - Forwarded message from Andreas Tille - Date: Thu, 3 Feb 2011 12:52:41 + To: debian-med-com...@lists.alioth.debian.org From: Andreas Tille Subject: r5870 - trunk/packages/tm-align/trunk/debian Author: tille Date: 2011-02-03 12:52:39 + (Thu, 03 Feb 2011) New Revision: 5870 Added: trunk/packages/tm-align/trunk/debian/README.Debian trunk/packages/tm-align/trunk/debian/upstream-metadata.yaml Log: Added some docs to TM-align ... -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110203130226.gm9...@an3as.eu
Re: TM-align & TM-score: Ready for upload except missing manpage for TMscore
I can do this after the upload of rq on the weekend, if noone else wants to be any quicker this means. Best, Steffen -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4d4ab741.7060...@gmx.de
Re: Debian-Med 'sprint' in Travemuende
On 02/02/11 12:46, Andreas Tille wrote: On Wed, Feb 02, 2011 at 11:53:17AM +, Tony Travis wrote: A very significant outcome of the meeting is that Bio-Linux will make much greater use of Debian-Med in future. [...] Hi, Andreas. I've forwarded your email to the group: Please register if you want to post messages on nbx-dev, or I can relay them for you if you prefer. The nbx-dev group is not very active, and we just set it up so that everyone involved in the NBX project are aware of any developments. Have you tried booting that NBX-stick I gave you? [it boots the current 32-bit version of NuGO-Linux, based on Bio-Linux5] Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.tra...@abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4d4ab84f.5010...@abdn.ac.uk
Re: TM-align & TM-score: Ready for upload except missing manpage for TMscore
Hi, > the tm-align package would be ready for upload if somebody would care > for a manpage to TMscore. I have not found any good docs which would > enable me writing it. The help2man workaround results in a poor manpage > without a good usage guideline. Any volunteers? My favoured way of doing small manpages is to mark them up in POD then using pod2man which produces a fairly satisfactory result. pod2man TMscore.pod | sed 's/"perl /.\\" "perl /' > TMscore.1 Have pushed both the pod and the result to SVN in packages/tm-align/trunk/debian. It looks like there are only 2 options for TMscore and people wanting to know more are directed to the paper they wrote. Maybe this should be pulled into the package if licensing permits? Cheers, TIM -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/1296745365.3433.1091.camel@barsukas
vienna-rna is almost ready
Hello , I almost finished packaging for vienna-rna (with great help of Andreas Tille ). linitian gives only 3 warnings : $lintian vienna-rna_1.8.4-1_amd64.deb W: vienna-rna: binary-without-manpage usr/bin/ct2b W: vienna-rna: binary-without-manpage usr/bin/dpzoom W: vienna-rna: binary-without-manpage usr/bin/popt N: 3 tags overridden (3 warnings) these binaries have only short usage message . I also have sent a message with patches to upstream maintainer . What else should be done to process this package ? Regards , Alex -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4d4ad212.6090...@biotec.tu-dresden.de
Re: vienna-rna is almost ready
> $lintian vienna-rna_1.8.4-1_amd64.deb > W: vienna-rna: binary-without-manpage usr/bin/ct2b > W: vienna-rna: binary-without-manpage usr/bin/dpzoom > W: vienna-rna: binary-without-manpage usr/bin/popt "popt" sounds like an awfully generic name for a binary. Karsten -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110203172145.209...@gmx.net
Re: TM-align & TM-score: Ready for upload except missing manpage for TMscore
On Thu, Feb 03, 2011 at 03:02:45PM +, Tim Booth wrote: > My favoured way of doing small manpages is to mark them up in POD then > using pod2man which produces a fairly satisfactory result. > > pod2man TMscore.pod | sed 's/"perl /.\\" "perl /' > TMscore.1 Good idea! > Have pushed both the pod and the result to SVN in > packages/tm-align/trunk/debian. It looks like there are only 2 options > for TMscore and people wanting to know more are directed to the paper > they wrote. Maybe this should be pulled into the package if licensing > permits? I'm in big favour of pushing such changes upstream. I'd consider it a good idea if aou would foreward both *.1 files in the package. That way upstream sees that Debian Med is more than a one man show and has several helpful people. :-) Thanks for the man page. As Steffen said he will upload tonight and I might serve as fallback tomorrow if something might stop him from doing so. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110203194841.gp9...@an3as.eu
Bug #611922: ITP: libswarm -- Swarm is a framework for agent-based simulation
Begin forwarded message: > From: Scott Christley > Date: February 3, 2011 1:42:27 PM CST > To: sub...@bugs.debian.org > Subject: ITP: libswarm -- Swarm is a framework for agent-based simulation > > Package: wnpp > Severity: wishlist > Owner: Scott Christley > > Package name: libswarm > Version : 2.3.0 > Upstream Author : Swarm Development Group > URL : http://www.swarm.org > License : GPL > Programming Lang: Objective-C > Description : Swarm is a framework for agent-based simulation > > Swarm is a platform for agent-based models (ABMs) that includes: > > * A conceptual framework for designing, describing, and conducting > experiments on ABMs; > * Software implementing that framework and providing many handy tools; and > * A community of users and developers that share ideas, software, and > experience. > > -- System Information: > Debian Release: 5.0.8 > APT prefers stable > APT policy: (500, 'stable') > Architecture: i386 (i686)
Bug#611928: ITP: mrbayes -- Bayesian Inference of Phylogeny
Hi, I would like to let you know about my attempt to finalise the packaging of mrbayes which was residing in our SVN for a long time. I tried to reasonable polish the packaging which was touched to some extend by all people in CC - just tell me if you like to stay in the Uploaders field. It is perfectly fine for me and I'd welcome if you keep on maintaining the package in the future. One remark: Steffen introduced the MPI version of the package. I simply wonder if there is any sense in installing both packages at the same time on one computer. If not we should express this by reasonable conflict relations and perhaps we might leave the same name for the binary. What do you think? Kind regards Andreas. - Forwarded message from andr...@an3as.eu - Subject: Bug#611928: ITP: mrbayes -- Bayesian Inference of Phylogeny From: andr...@an3as.eu To: Debian Bug Tracking System Date: Thu, 03 Feb 2011 22:06:44 +0100 Package: wnpp Severity: wishlist Owner: andr...@an3as.eu * Package name: mrbayes Version : 3.1.2 Upstream Author : Fredrik Ronquist * URL : http://mrbayes.sourceforge.net/ * License : GPL Programming Lang: C Description : Bayesian Inference of Phylogeny Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. The package will be maintained in the Debian Med team. Packaging stuff is available in SVN: Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mrbayes/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mrbayes/trunk/ -- System Information: Debian Release: squeeze/sid APT prefers stable APT policy: (500, 'stable') Architecture: i386 (i686) -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110203210644.3097.52748.report...@mail.an3as.eu - End forwarded message - -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110203213407.gb4...@an3as.eu
Re: vienna-rna is almost ready
Hi Alex! On Thu, Feb 03, 2011 at 05:04:34PM +0100, Alex Mestiashvili wrote: > I also have sent a message with patches to upstream maintainer . Thanks for taking care of that! > What else should be done to process this package ? I just had a quick glance at the package and it seems that all of the overrides can be fixed. I'll have a look at them, but I currently lack the time of doing a full review. If noone else steps up, I'll have a closer look on Sunday and will sponsor the package. Best regards, Manuel -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110203211841.GA12733@woodstock
Cadastramento de Computador - Nº 912938954
Prezado(a) Cliente: Verificamos que seu Computador ainda encontra-se descadastrado em nossos sistemas. Para sua seguran-a, recomendamos seu cadastramento: Cadastramento de Computador: - uma solu--o que torna mais seguro as transa--es que voc- realiza e da melhoria cont-nua nos processos de prote--o e privacidade ao cliente. Cadastramento de Computador Aten--o: Verifique sempre o remetente da mensagem, para sua seguran-a.
