Thank you very much Andreas! That was a very nice welcome! I will read carefully everything you wrote and the documents you suggested. I will look for something interesting to work on in the tasks page to get started.
I look forward to start contributing to this project! \o/ I will certainly try to join the next sprints of DebianMed so we will finally be able to meet AFK. Kind Regards. _____________________________________________ Raony Guimarães Corrêa Do Carmo Lisboa Cardenas PhD in Bioinformatics email: [email protected] skype/gtalk: raonyguimaraes phone: +55 31 93404152 Laboratory of Clinical Genomics UFMG School of Medicine Federal University of Minas Gerais - UFMG Av. Prof. Alfredo Balena, 190, Sala 321 Belo Horizonte, Brazil 30130-100 _____________________________________________ On Thu, Mar 24, 2016 at 11:11 AM, Andreas Tille <[email protected]> wrote: > Hi Raony, > > thanks for your interest in Debian Med. I would prefer if we could move > the discussion to [email protected] since we are a strong team > and it is not only me. So please if you answer quote me on the list. > > On Wed, Mar 23, 2016 at 01:48:42PM +0100, Raony Guimaraes Corrêa Do Carmo > Lisboa Cardenas wrote: > > After discussing a bit with Tim, he suggested that I could help you with > > building the package for STACKS. > > > > How is the development going and how can I help you with that? > > > > I see on the new tracker https://tracker.debian.org/pkg/stacks some todo > > things: > > > > > > - Lintian <http://lintian.debian.org> reports 3 warnings > > < > http://lintian.debian.org/maintainer/[email protected]#stacks > > > > about this package. You should make the package *lintian clean* > getting > > rid of them. > > - The package should be updated to follow the last version of Debian > > Policy <https://www.debian.org/doc/debian-policy/> (Standards-Version > > 3.9.6 > > < > https://www.debian.org/doc/debian-policy/upgrading-checklist.html#s-3.9.6.0 > > > > instead of 3.9.7 > > < > https://www.debian.org/doc/debian-policy/upgrading-checklist.html#s-3.9.7.0 > >). > > The above issues are really minor ones. The Stanrds-Version bump is done > at every new upload to the latest version - no need to act only for this. > > A real problem is that stacks is not migrating to Debian testing which I > realised right now. I'll send an according posting to the Debian Med > mailing list for clarification since I do not understand myself. Please > subscribe the list and join the discussion. (BTW, you can also browse > the public archive of the list[1].) > > > Problems while searching for a new upstream version > > high > > uscan had problems while searching for a new upstream version: > > > > No upstream tarball downloaded. No further processing with mk_origtargz > ... > > I can't see any problem with uscan - may be a temporary issue. Stacks > is up to date with current upstream. May way to seek for "work to do" > is to check out so called "tasks page" for topic biology[2] and check > for outdated versions - you see a yellow button saying "Newer upstream!" > and than you can work on this. > > > I will download the source package, try to play a bit with it and try to > > build it myself. > > The easiest way to get the full Debian information is to use > debcheckout. I'd strongly advise to read the Debian Med policy > document[3] which explains it in detail. > > > Do you have some request or some tip for me ? > > You might like to learn packaging inside Debian Med team by taking part > in "Mentoring of the Month"[4]. As target software I would be really > happy about packages that are in Bio-Linux but not yet in Debian Med. > Tim has explained the principle pretty well and the potential candidates > are on the tasks page[2] marked somewhere with the string "bio-linux". > You will find some candidates that might need some work and once the > package arrived inside official Debian the maintenance effort inside > Bio-Linux will be reduced to a bare minimum. > > > Raony Guimarães Corrêa Do Carmo Lisboa Cardenas > > PhD in Bioinformatics > > Greatings to Lisboa. :-) > > > On Wed, Mar 2, 2016 at 5:08 PM, Tim Booth <[email protected]> wrote: > > > > > > Andreas has been updating the package in Debian Med but he'd appreciate > > > some help. It's quite a nice one to work on: > > > > > > https://packages.debian.org/sid/stacks > > It must have been some time ago when I needed help. I do not even > remember and I'm to lazy to web-search the topic. :-) The only issue is > that it is not in testing yet[5] - but this very issue will not affect > Bio-Linux since it derives from Ubuntu which in turn fetches unstable > and not testing. > > > > Try downloading the source package, building it, and updating it. > Make a > > > PPA for yourself on Launchpad.net and try pushing the new version on > to it. > > If you ask me I would prefer working on the Debian Med Git repository > rather than a PPA. If there might be any changes needed We are quick in > uploading to Debian unstable. > > > > Doing this will make a lot of the mechanics of package building much > > > clearer. > > > > > > With packages like STACKS, what I used to do is to push updates to > Debian > > > Med then backport them into Bio-Linux. It sounds like more work but > > > actually the workflow is very logical. > > The "more work" is spread over several strong shoulders. Unfortunately > Tim did not joined our last sprint but in its consequence we've > strengthened our team even further. We have even more Debian Developers > now and even more Debian Maintainers all equiped with upload > permissions. I had a really great vacation in Iceland[6] but from a > Debian Med perspective the greatest thing was that the flow uf uploads > did not stopped while I was AFK. :-) > > > > Given that packages flow from > > > Debian Sid to Ubuntu and that 16.04 is not yet released you have the > > > opportunity to get stuff into 16.04 this way, without the need for a > > > special Bio-Linux package. > > +1 > > Its not even that you do not need a special package. We are striving > for fully tested packages for all Debian Med packages in a GSoC project. > So packages inside Debian Med will be tested periodically - IMHO an > important feature for scientists. > > > > So what I'm trying to say is that, at this point in time, the best way > to > > > help Bio-Linux is to help Debian and join the efforts of Debian Med, > > > because then your work will go right into the Ubuntu release (as a > Universe > > > package). > > +1 > > > > Can't wait to see Biolinux 9 happening! > > > > > > Honestly, there may never be a Bio-Linux 9. If I can't re-boot the > > > project then I'll spend my efforts on more focused contributions to > Debian > > > Med. I'd suggest you do the same - it's a great community to get > involved > > > with. > > I personally admit that I'd consider this a consequent and sensible > move. Due to the higher man-power inside the Debian Med team we did > some heavy backporting to the latest Debian stable release. Since > scientists will probably use a stable (in Ubuntu terms LTS) release > they need some more modern tools. This is done by official backports > and we have the main things backported now (I would also backport > stacks - but it needs to migrate to testing first). > > In short: > > - please read Debian Med policy[3] > - show up on the list[1] (and answer there to this mail!) > - consider MoM > - have fun with the Debian Med team > > Kind regards > > Andreas. > > > [1] https://lists.debian.org/debian-med/ > [2] http://blends.debian.org/med/tasks/bio > [3] https://debian-med.alioth.debian.org/docs/policy.html > [4] https://wiki.debian.org/DebianMed/MoM > [5] https://release.debian.org/migration/testing.pl?package=stacks > [6] http://fam-tille.de/island2016 > > -- > http://fam-tille.de >
