[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: Outreachy current



Hello all,

I have no idea about how much this suits the concepts behind Outreachy,
but there is a list of packages missing for this
https://bcbio-nextgen.readthedocs.io/en/latest/ software. It is about
getting DNA/RNA sequence data from patients/healthy human controls and
interpret it. I mean - we have bcbio as a package in Debian, but for all
the flavours of workflows that it offers, there is more to be done.
Michael screened the source code for this and came up with
https://salsa.debian.org/med-team/bcbio/blob/master/debian/TODO .

So, I would be very happy for

 * packages from that list being added to Debian (there are a few
presumed easy targets like |https://github.com/vals/umis|, medium
difficult ones like  |https://github.com/gt1/biobambam2) Others are not
necessarily more difficult, just these may add additional packages in -
SnpEff addressed by Andreas is such a case, weird ones like
|||https://github.com/brentp/mosdepth that uses the programming language
nim)|.
|

| * assessments how far we get with the current bcbio package for
routine bits|

|Best,|

|Steffen
|


On 22.03.19 11:09, Saira Hussain wrote:
> ---- On Wed, 20 Mar 2019 09:43:43 +0000 *Liubov Chuprikova
> <chuprikovalv@gmail.com>* wrote ----
>
>     Hi Saira,
>
> Hi Liubov,
>
>
>     I am glad to know there is a new potential Outreachy student! :-)
>
> me too :) 
>
>
>     On Tue, 19 Mar 2019 at 09:13, Andreas Tille <andreas@an3as.eu
>     <mailto:andreas@an3as.eu>> wrote:
>
>         On Mon, Mar 18, 2019 at 11:11:11PM +0000, Saira Hussain wrote:
>
>         > What's the best way to use autopkgtest locally to emulate
>         the test? As I currently
>         > only treat them as  sh scripts and test manually.
>
>         I admit I do it that way most of the time. ;-)  I also added a
>         pbuilder
>         hook for testing.  Pbuilder is a tool which builds Debian
>         packages in a
>         minimalistic chroot environment and thus the test is done in a
>         chroot
>         (but obviously did not fetched that last error - no idea why).
>
>         I once followed
>
>            https://wiki.debian.org/DebianScience/Debci
>
>         (see paragraph "Configure your system to run autopkgtest using
>         lxc")
>         but dealing with those lxc containers was not always easy and
>         after I
>         had some trouble I stopped this again (lazy me :-().
>
>         I've put Liubov (last years outreachy student) in CC - may be
>         she has
>         some additional hints.
>
>
>     In case, you haven't found this already, here [1] you can read how
>     to run autopkgtest using different virtualizations (it's almost
>     the same actually that is in /usr/share/doc/autopkgtest
>     directory). I am using schroot, but I cannot say that it's the
>     best choice since I haven't tried others. It's up to you what to
>     choose :-)
>
>     Most of the time you don't need to build the packages locally,
>     just run the tests you wrote with packages from distribution:
>
>     autopkgtest -B packages/mysrc -- /virt-server/
>
>     But in case there are other unreleased changes in the package (for
>     example, you have added new test data), as Andreas mentioned
>     already, you may need pbuilder or sbuild to build packages in a
>     chroot environment and then to run tests. I am using sbuild, so I
>     put a couple of useful links below related to sbuild [2][3]. You
>     may find some configuration examples in my ansible recipies [4].
>     Here is some additional information on writing autopkgtests that
>     was useful for me [4].
>
> Thanks a lot for your Vagrant! That something very valuable and it's
> amazing you're sharing :) 
>
>
>     If you have any questions, feel free to ask.
>
> That covers me for the moment but I may do in future!
>
>
>     Have fun and all the best,
>
> Thanks a lot :))))
> SH
>
>     Liuba.
>
>
>
>     [1] https://people.debian.org/~mpitt/autopkgtest/README.running-tests.html
>     [2] https://wiki.debian.org/mk-sbuild
>     [3] https://wiki.debian.org/sbuild
>     [4] https://github.com/liubovch/vagrant-debianVM/blob/master/playbook.yml
>     [5] https://ci.debian.net/doc/file.TUTORIAL.html
>
>
>


Reply to: