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Re: Packaging "AGAT - Another Gff Analysis Toolkit "



Hi Andreas,


On 10/22/20 3:29 PM, Andreas Tille wrote:
Hi again,
Ok. got it.
I tried to fix pristine-tar.  You should *not* manually add complete
tarballs there.  Also the tarball is *without* the Debian revision - so
the name should be agat_0.5.0.orig.tar.gz (and not
agat_0.5.0-1.orig.tar.gz)  Please re-read the recommendations from
MoM and the Debian Med policy.  Its finally important that you can
successfully do `gbp buildpackage` - if it works for you to recreate
the tarball it works for others as well.
I have removed d/tests.
Regarding the packaging:  It contains the unchanged autopkgtest
boilerplate.  Please either provide a sensible autopkgtest or remove
the boilerplate debian/tests.

They dont have a formal (paper) citation, only https://zenodo.org/record/4044553.

I have added agat to conda - metadata.

So you know some citation about agat?  This would be great.  There is
also the Conda ID "agat" which you could specify in
debian/upstream/metadata (see template).
should be done.
You should also provide a lintian override for
script-with-language-extension lintian warning (there exist a proper
example to do so in the Debian Med template!)

should be done.

I still get lintian issues "bad-whatis-entry" that I am now running out of options on how to fix them. However, man displays

a ok page (in my eyes).

Please also fix the incorrect-path-for-interpreter - just check the
rules file of package sspace or vcftools for example.  There are also
some manpage errors mentioned by lintian.  Please try to fix these.

Kind regards

       Andreas.

On Thu, Oct 22, 2020 at 02:06:47PM +0200, Andrei Rozanski wrote:
Hi Andreas,


Thanks for the replying even in "real life mode" :D


On 10/21/20 10:53 PM, Andreas Tille wrote:
Hi,
Thanks for pointing that out. I have pushed it.
very short notice (I'm in real life mode this week):  The pristine-tar
branch is missing agat_0.5.0.orig.tar.gz.

Kind regards

          Andreas.

On Wed, Oct 21, 2020 at 06:44:54PM +0200, Andrei Rozanski wrote:
Hello,


I have worked on AGAT (https://salsa.debian.org/med-team/agat). For the
moment, lintian seems fine. The build also looks promising.

I would like to request some help for checking/guidance on what I have done
so far.


Many thanks.

Best,
AndreiR

On Fri, Oct 16, 2020 at 7:41 AM Andrei Rozanski <rozanskide@gmail.com>
wrote:

Hi Andreas,

Thanks for the answer! I will work on it.



On October 16, 2020 07:39:23 Andreas Tille <andreas@an3as.eu> wrote:

Hi Andrei,
On Fri, Oct 16, 2020 at 07:30:11AM +0200, Andrei Rozanski wrote:

More recently I have tried AGAT - Another Gff Analysis Toolkit
(https://github.com/NBISweden/AGAT) and found it quite useful in
general. I
have failed to find a debian package for it.

Would it be ok for me to try to package it or should I prioritize the
COVID
list and do AGAT later?

The general rule is: We package what we use.  So yes, just go for it.
(May be those who assembled the COVID list did not had this on the
radar?)

Feel free to keep on asking here in case of trouble.

Thanks a lot for your contribution

       Andreas.

--
http://fam-tille.de

Best
AndreiR

--
Andrei R

Many thanks !

Best

AndreiR


Thanks!

Best

AndreiR


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