On Tue, Mar 18, 2014 at 10:12 PM, Yaroslav Halchenko <deb...@onerussian.com> wrote: > - QA, such as build time testing: cannot be stressed enough on its > importance for anyone at least whispering about 'reproducibility'. >
I would definitely prepare good material talking about 'reproducibility'. More below. >> Any suggestions on something fancy to display would be helpful. > > Fancy... hm... I some times like to amuse "reproducibility-eager" folks > with commands such as > > debootstrap --arch=i386 --include=python potato /tmp/potato > http://archive.debian.org/debian > > which in tandem with schroot could be used to bring Debian release from > decade(s) back with > > novo(potato):~ >>gt; python > Python 1.5.2 (#0, Dec 27 2000, 13:59:38) [GCC 2.95.2 20000220 (Debian > GNU/Linux)] on linux2 > Copyright 1991-1995 Stichting Mathematisch Centrum, Amsterdam > This is interesting. Reproducibility is one reason I believe the Galaxy Project[1] doesn't favor using a stablished package manager and are trying to build their own[2][3](or maybe an abstract meta-package-manager). I wonder if they could integrate something like this to satisfy their reproducibility requirements. I lost some of my initial excitement about contributing to Debian Med. If I cannot use the results of my effort in the system where I actually do my job, there is not much to gain from my time devoted to Debian Med. Then there are options like linuxbrew(homebrew port to linux) with a much lower initial barrier for contributions. Way simpler to write a formula compared to a DEB. I believe the Debian way is superior to anything out there. With higher standards and quality assurances. But I cannot see more people using it if projects like Galaxy or CloudBioLinux don't fully embraced. It is quite sad they haven't. [1]http://galaxyproject.org/ [2]http://dev.list.galaxyproject.org/tool-dependencies-xml-format-td4661410.html [3]http://dev.list.galaxyproject.org/Better-packaging-for-toolshed-binaries-td4661447.html [4]http://cloudbiolinux.org/ Best, Carlos On Tue, Mar 18, 2014 at 10:12 PM, Yaroslav Halchenko <deb...@onerussian.com> wrote: > Hi Steffen, > > On Tue, 18 Mar 2014, "Steffen Möller" wrote: >> I was invited to a local (Northern Germany) workshop on next generation >> sequencing >> https://sites.google.com/site/nexgenseqmv/home/workshop >> to give a quick overview on what Debian/Ubuntu/BioLinux can do for them. >> This is a very friendly environment and besides >> * explaining how community-run Linux distros work >> * that Linux not necessarily means desktop, >> - but may mean virtual >> - or server and that >> - all major cloud services feature Debian images > > Do not be shy here: by working "in Debian" we are pretty much automagically > benefiting from the work of more 'cloudy' people cooking up all the appliances > etc. Thus there is a huge benefit from sharing > expertise/responsibilities across different teams. That is why work of Debian > Med is automagically omni-present through-out all possible deployment > scenarios > -- from cell phones (may be not by Debian itself, but by its derivative(s)), > to > servers, clusters, "mainframe" architectures which might not even be generally > available (s390x, sparc) to regular mortals, and all possible clouds. > >> * what Blends are >> * what packages are available for Next Generation Sequencing > >> I am very eager to learn about what the audience expects from our distro(s). > > I would also emphasize on unique "features" of Debian such as > > - clear open standards (thus packaging is done "the right way" which > contributes to packages longevity) > > - licensing "clearing house": helps with wider adoption and longevity > of software itself > > - QA, such as build time testing: cannot be stressed enough on its > importance for anyone at least whispering about 'reproducibility'. > >> Please kindly mention whatever issue is close to your heart that should >> be presented. I was very happy about the recent advent of the IGV. > >> To have something tangible, I asked Roland from Qlustar.com to >> demonstrate over the coffee breaks how to set up a distributed work >> environment with Debian. Tony had found and introduced their >> technology for the Debian Med Sprint. He kindly agreed, so we will >> jointly learn about how NGS-savvy wet-lab biologists are approaching >> us. > > heh -- never heard about qlustar... interesting to hear what you learn > from the coffee break > > but also do not forget that Debian itself comes with many open HPC > related projects such as batch systems etc: > http://blends.debian.org/science/tasks/distributedcomputing > >> Any suggestions on something fancy to display would be helpful. > > Fancy... hm... I some times like to amuse "reproducibility-eager" folks > with commands such as > > debootstrap --arch=i386 --include=python potato /tmp/potato > http://archive.debian.org/debian > > which in tandem with schroot could be used to bring Debian release from > decade(s) back with > > novo(potato):~ > $> python > Python 1.5.2 (#0, Dec 27 2000, 13:59:38) [GCC 2.95.2 20000220 (Debian > GNU/Linux)] on linux2 > Copyright 1991-1995 Stichting Mathematisch Centrum, Amsterdam > > > if you want to impress them even a bit more -- you could use apt-cacher-ng and > then debootstrap right there in matter of seconds (depending on your > harddrive/cpu speed) + pre-cooked schroot and you can really get them back > into > the past ;) JUST MAKE SURE YOU HAVE ENOUGH DISK SPACE (do not ask why it is > in capitals) > >> I would otherwise just dig into the data we are producing locally >> and show something. > > So overall -- press not as much on flashiness (on-a-knee projects might be > flashier) but rather on long standing standards, quality, pervasiveness, > shared > responsibility, impact. > > if really bored, you can even watch my talk a year back, although I think > I have done much better ;-): > http://sea.ucar.edu/event/open-not-enough-benefits-debian-integrated-community-driven-computing-platform > > My 1c ;) > > -- > Yaroslav O. Halchenko, Ph.D. > http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org > Senior Research Associate, Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 > WWW: http://www.linkedin.com/in/yarik > > > -- > 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/20140319021212.gn28...@onerussian.com > -- 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/cabgghbkk2pjls1xewjrt66ycox8dtg7e2ixcc5qxxh0s+k1...@mail.gmail.com