Re: IBDA for Debian
Hi Yu,
On Fri, Feb 14, 2014 at 07:34:24PM +0800, Yu PENG wrote:
> Sure. Please let me know when it is available in debian, I will do the
> test.
:-)
> I will also work on the test suite in the meanwhile. What kind of
> test are you looking for? Is there any document about that?
We somehow need some script feeding a certain data set into idba and
compare the result with something that is expected. The data set should
be freely available, not extraordinary large and somehow typical for the
application.
Thanks for your support
Andreas.
> On Fri, Feb 14, 2014 at 3:31 PM, Andreas Tille <andreas@an3as.eu> wrote:
>
> > Hi Yu,
> >
> > thanks for your kind reply.
> >
> > On Fri, Feb 14, 2014 at 11:15:10AM +0800, Yu PENG wrote:
> > > I will be more than happy to help you on this. IDBA is an open source
> > > assembler developed by our group (
> > > http://i.cs.hku.hk/~alse/hkubrg/projects/idba/). Originally, it only
> > > supported single-end genomic data, and later we added support for
> > > meta-genomic, single-cell and transcriptome. idba-1.1.1 is the latest
> > > version which contains all the tools. IDBA is released under GPL V2,
> > please
> > > feel free to fetch the idba-1.1.1 package from google code page you
> > > mentioned.
> >
> > Great. I can confirm that the package arrived in the Debian New queue:
> >
> > http://blends.debian.org/med/tasks/bio#ibda
> >
> > > Note that we don't really use the svn provided by google code,
> > > but only use the downloads to hold the release tar.
> >
> > That's perfect. Usually we always try to base a Debian package on a
> > released version. Using an version control system extract is only done
> > if the authors do not maintain versioned releases. So we are really
> > happy about your way to distribute ibda.
> >
> > > Please let me know if you need any other information/code change to make
> > it
> > > available in debian.
> >
> > I hope that the package will be accepted in the next couple of days.
> > It would be great if you or some colleage of you who might use Debian
> > or any derivative would test it.
> >
> > Moreover Debian is implementing tests which are running over the whole
> > archive regularly. It would be great if you could provide some small
> > test suite with free and not so large data we could use to verify the
> > correctness of the results.
> >
> > Many thanks for your support
> >
> > Andreas.
> >
> > --
> > http://fam-tille.de
> >
> >
--
http://fam-tille.de
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