Re: [MoM] Fwd: Outreachy 2016 application

Hello Andreas!

Sorry for the delay, but it seems like I struggle with the setup and I can't resolve it by myself.

Thanks for the advice about building packages -- configuring pdebuild really helped and I build all the mentioned packages by editing debian/gbp.conf as Debian Med Policy document recommends.

I read carefully the CI documentation and followed all the steps (I chose lxc backend. I created /etc/sudoers.d/lxc file as described and ran debci setup), but I'm still not able to run tests.

Here is the executed command:
anna@debian:~/projects/aegean$ adt-run --user debci --output-dir /tmp/output-dir/ ./aegean_0.15.1+dfsg-3_amd64.changes --- lxc --sudo adt-sid-amd64

I got the following error: "Error: container adt-sid-amd64 is not defined"

This discussion looks relevant, but the executed command here is slightly different.

Do you have any ideas how to fix this issue? What am I doing wrong?

I'll keep in mind that the next package after bwa is prodigal, but I guess I'll have more questions about the first one and the process as a whole. The acquaintance stage is always time consuming

Regards,

Anna

2016-02-20 13:54 GMT+03:00 Andreas Tille <andreas@an3as.eu>:

Hi Anna,

On Sat, Feb 20, 2016 at 11:36:05AM +0300, Anna Lioznova wrote:
> Hello, Andreas!
>
> I just wanted to give you a small update: I'm working on the task, but I
> have not finished it yet.
> Yesterday I installed Debian on my laptop (which was a bit tricky, but
> finally I managed), so I'm exploring it.
>
> gbp buildpackage
> doesn't work for me, but the manual
> <https://www.debian.org/doc/manuals/maint-guide/build.en.html> says to use
> -uc -us options, which help

I do not think that this is needed (I never use these uptions). You
might like to check again in Debian Med policy - perhaps by seeking for
the string gbp - specifically the paragraph
"To make gbp buildpackage build the package with pdebuild."

> I'm in progress with reading about Debian CI.
> Thanks for the examples and for all the details -- I like learning this way
> too. I'm in progress with tests also.
>
> Thanks again for such a detailed letter and for your time, that's very
> helpful! The plan looks clear and I don't have any questions now.

Sounds good. Just feel free to keep on asking if a question might arrise.
Chances are good that some other helpful member of the team might answer.

I've found another candidate package lacking a test suite which you
might like to takle right after bwa. I just updated prodigal and in
preparation of your work moved the packaging from SVN to Git. The doc
contains the hint:

prodigal -i my.genome.fna -o my.genes -a my.proteins.faa
prodigal -i my.metagenome.fna -o my.genes -a my.proteins.faa -p meta

So your task would be to find such my.* files, provide these for the
package and run the commands as a test suite.

> I hope to cope with this task in a couple of days (I don't have that much
> spare time because of work and classes)

That's fine. Just make sure your classes have preference over this GSoC
project. From my point of view the advantage of this specific project
over others I was working in as a mentor is that you have quite small
chunks of work which can be finished step by step.

Kind regards

Andreas.

--
http://fam-tille.de