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Re: Presentation of Debian Med on local Next Generation Sequencing workshop (April)



Le Wed, Mar 19, 2014 at 10:20:33PM -0400, Yaroslav Halchenko a écrit :
> 
> upon brief look: I have apt-get sourced cufflinks -- found no
> unittests available
> 
> the same for tophat

Hi Yaroslav,

yes, unit tests are not always available, but I see more and more editorials in
top journals advocating “reproducible research”, so I think that more and more
bioinformaticians will be able to convince their managers to work on unit
tests.  It is very good that in Debian we have the autopkgtest infrastructure
growing at the same time.

For packages without upstream tests, in the meantime, even the most simple
tests like running the command with the --help option, are potentially useful.
My favorite example is T-COFFEE, where we were distributing a 100 % broken
package on arm for years.  With autopkgtest, we will have a better overview on
what package works where (just a successful build is not enough), and this will
help people to evaluate the feasiblity of projects based on Debian on amd64,
and also on more rarely used platforms (such as the Raspberry Pi as we read on
this list).

Slightly more complex tests can often be built from the examples in the
program's README.  On my side, I am still on a learning phase with autopkgtest,
but I hope that collectively we will have a clear vision on what to recommend
Upstream so that they can write or accept user-contributed tests are trivially
run by autopkgtest.

I also like a lot the “litteral programming” side of the “reproducible
research” trend.  I am developing some tutorials based on real data analyses
from my work, which are currently implemented in knitr
(http://yihui.name/knitr/), and which I hope to iron out so that they can be
used to test a Debian image in an integrated way.  However, they currently
still use programs that are not yet packaged.

Work in progress but comments welcome !  https://github.com/charles-plessy/tutorial

Cheers,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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