Dear Andreas,

Thank you so much for all your comments! I confirm i pushed the changelog
entry , i hope i did it right ;)

I would love to go on with adding an autopkgtest to another package, i was
thinking to continue with rsem (n.890792
<> ), if that is ok
for everyone!

I would also kindly like to express my interest to apply to either
outreachy or GSoC. I had a look to the Outreachy announcement for this
round of applications and as i did not see any proposed project by the
debian med team (especially the one about adding autopkgtest suites),  i
was thinking about the GSoC as an alternative. As my PhD thesis will be
ready in the end of March but i will still be a student until the beginning
of June, i was thinking if it would be possible for me to apply.

Anyway, apart of the internships, i would like to continue contributing to
the debian med project , it is a truly unique experience!

Thank you so much again for all the help and comments!

Kind regards,

On Mon, Feb 19, 2018 at 11:01 AM, Andreas Tille <> wrote:

> Dear Kate,
> On Mon, Feb 19, 2018 at 12:21:35AM +0200, Kalou.Katerina wrote:
> > Thank you for your comments!! I tried to push the files again , i think
> > that now it worked :)
> I confirm the push worked now.  I've pushed some more commits - partly
> related to your work.  Please keep on reading my comments below.
> > > > Any
> > > > comments and corrections will be much welcome!! In my linux machine
> the
> > > > 'autopkgtest -- null' command reports a pass.
> > > >
> > > > In the example folder i have put two sample data that i managed to
> found
> > > at
> > > > ''. These two files are '.BED'
> file
> > > > extensions. The example at the macs package install instructions is
> using
> > > > the 'BAM' extension , if anyone has any recommendation on where to
> find
> > > > these, it will be much appreciated!! :)
> > >
> > > In any case make sure you document the origin of the example filese in
> > > debian/README.source (may be you add your question also in this file).
> I've seen you have give some (rather vague) pointer in README.test
> (which is fine - no need to create an extra README.source.  Besides the
> fact that all Debian related stuff needs to be in debian/ dir (I just
> moved the file) I wished you would add some more specific pointer.  The
> best thing would be something like
>     wget URL_to_example_file1
>     wget URL_to_example_file2
> So everybody can immediately reproduce what you did to get the files.
> To express what I mean I did so in the latest commit.  I also left the
> files compressed as downloaded which requires an extra file
>     debian/source/include-binaries
> (dpkg-buildpackage will tell you about this so this is no knowledge you
> need to keep by heart. ;-) )
> Regarding how to get BAM files instead of BED files I'm hoping for
> comments here on the list but for the moment macs2 seems to do something
> sensible which should qualify for a first test.
> > > > Finally , i included the files 'README.test',
> > > 'macs-example-data.install'
> The file macs-example-data.install is wrong.  In the other package you
> worked on we have created an extra data package.  I do not think that
> the amount of extra data in the macs example rectifies an additional
> package and thus we have no such package macs-example-data defined in
> debian/control.  Thus this file is simply ignored.  You rather need to
> put files in debian/macs.examples (and make sure those files are really
> existing - since I bumped debian/compat in some unrelated change
> mentioning non-existing files has lead to build problems).
> > > > and 'macs.install', taking inspiration from the previous packages
> like
> > > > rapmap i worked on. The purpose was to send the examples folder to
> the
> > > > 'usr/share/doc' directory during installation , i do not know if i
> did it
> > > > right!
> I've now fixed it - please check all my according commits.
> Finally please always add a changelog entry to the package documenting
> your changes.  I'd recommen to use the dch tool for this.  For instance
> you can do
>     dch --team "Add autopkgtest (Closes: #879622)"
> specifically the "Closes:" is important to automatically close the bug.
> (You can also use `dch --team` and add the string manually with the
> editor.)
> I would like you to take over the changelog entry (that's why the --team
> option - see `man dch`) since I want to give credit to the person who
> has written the test and has fixed the bug.
> I think the package is ready once you have done the changelog entry and
> I'll upload once I have seen your commit.  Yesterday I added a set of
> new bugs for packages in need of an autopkgtest.  So there is a plenty
> to pick from and as I wrote here before I issued an according GSoC
> project proposal (which can be also picked for outreachy as far as I
> know).
> Kind regards
>        Andreas.
> --

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