Re: SPAdes for Debian
Hi Anton, just to let you know that we are working on this. On Wed, Apr 02, 2014 at 02:51:32PM +0400, Anton Korobeynikov wrote: > >> 1. spades.py --test > >> 2. spades.py --iontorrent --test > >> 3. dipspades.py --test > >> > >> Probably you need only to look that it finishes w/o problems and the > >> final contigs file contains a single contig. > > > > Could you turn this result somehow into code that returns some true or > > false? > We will see what can be done here. Right now there will be non-zero > return code in case of any crash. But we'll also check the results. Thanks. > > Hmmm, could you please be more verbose about this. > Here it is: https://github.com/iontorrent/bamtools I noticed that some preparation for packaging was done in the past but stalled for unknown reason. I updated the packaging to the latest version but was running into some issues I need to sort out first. > > For sure we would > > like to package the most useful version. Any chance that the bamtools > > authors might adopt any relevant changes. What would you recommend to use > > for a Debian package? > Well, I do not know all the differences, in fact. We prefer to use > IonTorrent version because we know it's used in TorrentSuite and we > tend to play safe wrt (possible) incompatibilities :) Before I'll upload I'll do some investigation into this to check the difference. If it seems to be relevant - specifically to fit the needs for SPAdes without harming other compatibility - we might decide for this version as well. I would even try to contact both upstreams whether they might intent to merge their effort. Thanks for the hints 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: https://lists.debian.org/20140404090539.gc19...@an3as.eu
Re: SPAdes for Debian
Hi Andreas, >> > Could you turn this result somehow into code that returns some true or >> > false? >> We will see what can be done here. Right now there will be non-zero >> return code in case of any crash. But we'll also check the results. > Thanks. We already implemented the checking. So, it will be included into 3.1 :) -- With best regards, Anton Korobeynikov Faculty of Mathematics and Mechanics, Saint Petersburg State University -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/ca+ov9+k+1qhmhj1xadqrlg2e3mjurfuumc6tfvxiynn2vqk...@mail.gmail.com
Re: SPAdes for Debian
Hi Anton, On Fri, Apr 04, 2014 at 01:12:26PM +0400, Anton Korobeynikov wrote: > >> We will see what can be done here. Right now there will be non-zero > >> return code in case of any crash. But we'll also check the results. > > Thanks. > We already implemented the checking. So, it will be included into 3.1 :) Thanks a lot! 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: https://lists.debian.org/20140404094704.ge19...@an3as.eu
Re: [RMLL/LSM] - CfP 2014
Hi, The call for talks for LSM has been extended up to 15th April, please consider submitting talks! The health theme has not had many answers yet. Feel free to widely disseminate information and to motivate those who hesitate. I'll try to spread the CFP again and again. Regards, /Johan Le 02/04/2014 10:28, Emmanuel Promayon a écrit : >> I just submitted a Debian Med packaging workshop as I did in Geneva to >> do a life packaging demo again. I start to like this kind of demo and >> will do this also for Debian Science and Debian GIS. > > This is great. For the history books, Andreas and Mathieu started the > initial prep for the CamiTK package during our presentation at the > LSM2012. Without this we would probably had a very long steep learning > curve! Thumbs up. > > Best regards, > Mahnu > > -- > Emmanuel Promayon > UJF-Grenoble 1, CNRS, TIMC-IMAG UMR 5525 (équipe GMCAO) > Institut de l'Ingénierie de l'Information de Santé > Faculté de Médecine - 38706 La Tronche cedex - France > Tel. +33/0 456 52 00 03 - Fax. +33/0 456 52 00 55 - B7 > > 0x62073FE4.asc Description: application/pgp-keys signature.asc Description: OpenPGP digital signature
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, I guess Thorsten was asking this question wearing his ftpmaster hat. Any comment to his question? Kind regards Andreas. On Tue, Apr 01, 2014 at 02:55:44PM +0200, Thorsten Alteholz wrote: > Hi Stephen, > > lintian tells me something about: > W: phyutility: incompatible-java-bytecode-format Java7 version (Class > format: 51 > I am not a Java expert, but wouldn't this make the package unusable > on standard Debian? > > Do you need src/jade/lib/libmatrixExp.so for anything? > >Thorsten > > > -- > To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org > with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org > Archive: > https://lists.debian.org/pine.lnx.4.64.1404011451530.29...@tor.gallien.in-chemnitz.de > > -- 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: https://lists.debian.org/20140404135401.gb27...@an3as.eu
