Hi Raony,
thanks for your interest in Debian Med. I would prefer if we could move
the discussion to debian-med@lists.debian.org 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/debian-med-packaging@lists.alioth.debian.org.html#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for outdated versions - you see a yellow button saying "Newer upstream!"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 <avarus@fastmail.fm> 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