[Debian-med-packaging] ITP: scythe -- Bayesian adaptor trimmer

[Andreas Tille]

Hi Kevin,

On Wed, May 06, 2015 at 10:48:07PM +1000, daube wrote:
> I'm new to Debian packaging/development, and I'd like to start by
> packaging a useful piece of software for those using Debian in
> computational biology.

Thanks for your interest and introducing yourself with a ready package.
:-)
 
> I recently packaged scythe[0], a next-gen sequencing read adaptor
> trimmer written by Vince Buffalo. Scythe uses a Naive Bayesian matching
> algorithm to trim contaminants from sequencing reads. It is more
> accurate than other similar packages due to the probabilistic matching
> algorithm that it uses, which accounts for features of common DNA
> sequencing platforms. I have previously contributed code to scythe, and
> I believe I am sufficiently familiar with its development and code base
> to maintain this package.

It's very welcome to have people with deeper knowledge about the
upstream code in the packaging team.

> However I'm new to debian packaging, so any and all advice is
> appreciated!
> 
> The package has been uploaded to mentors.d.net:
> 
>     http://mentors.debian.net/package/scythe

Uploading to mentors is OK but our team workflow does not require this.
Usually we are sponsering right from the Git repository.

> I'm hosting the debian packging repo at:
> 
>     https://github.com/kdmurray91/scythe-debian

In our team we try to follow a strict policy[1] which implies to use Git
at git.debian.org.  This has several advantages - feel free to ask if
you have doubt about it and I'll come up with (hopefully) good reasons.

So I would like you to create an account on alioth.debian.org as advised
and become a member of the Debian Med team.  Once this is done you will
get commit permissions to the Debian Med Git.  Please note that it is
recommended to use pristine-tar for your Git repository (see the
relevant section).

>From a packaging point of view (without really trying to create the
package - just looking at the metadata) it looks quite good.  According
to our team policy you should

diff --git a/debian/control b/debian/control
index 8a0489c..33e75bc 100644
--- a/debian/control
+++ b/debian/control
@@ -1,5 +1,6 @@
 Source: scythe
-Maintainer: Kevin Murray <spam at kdmurray.id.au>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Kevin Murray <spam at kdmurray.id.au>
 Section: science
 Priority: optional
 Standards-Version: 3.9.6


and in debian/copyright I'm missing a section

Files: debian/*


Otherwise it seems to be fine.

Please do not hesitate to ask for further help here and thanks a lot
for your packaging work

    Andreas.

> [0]: https://github.com/vsbuffalo/scythe
[1] http://debian-med.alioth.debian.org/docs/policy.html

-- 
http://fam-tille.de