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Re: SPAdes for Debian

Hi Anton,

On Wed, Apr 02, 2014 at 01:45:32PM +0400, Anton Korobeynikov wrote:
> > It would be really great if you could provide such a suite which could
> > be a simple script processing your test data youo are providing anyway
> > and add a simple comparison mechanism to verify the result.  When I
> > worked on the 3.0.0 package (which unfortunately is not finished yet ...
> > exactly due to the reason that I stumbled upon some tests and wanted to
> > do more comparisons) I realised that some output files are containing
> > dates and time stamps and thus comparisons do not make any sense but
> > other files need to match.  I guess it would be on one hand easy for you
> > to define a valid test result and it would also be quite helpful for
> > your users.
> I believe that you need to run 3 cases:
> 1. spades.py --test
> 2. spades.py --iontorrent --test
> 3. dipspades.py --test
> Probably you need only to look that it finishes w/o problems and the
> final contigs file contains a single contig.

Could you turn this result somehow into code that returns some true or
> > In Debian we are maintaining libbam-dev (from samtools currently at
> > version 0.1.19-1).
> This looks like another package. I'm talking about
> https://github.com/pezmaster31/bamtools

Ahh, you are right.  The packaging was started[1] by Michael R. Crusoe
but is somehow stalled and went out of focus.  Michael (in CC) can you
please layout your plans whether you intent to continue this package?

> (actually, we're using
> IonTorrent fork which knows how to do multi-threaded processing).

Hmmm, could you please be more verbose about this.  For sure we would
like to package the most useful version.  Any chance that the bamtools
authors might adopt any relevant changes.  What would you recommend to
use for a Debian package?
> > So if you would give me permission I would bounce this mail to the list
> > and might do so in the future as well in case you might forget (you do
> > not necessarily need to be subscribed but please ask for beeing CCed
> > to receive direct answers to your mail).
> Sure!

Thanks - Done.

Kind regards and thanks for your cooperation


[1] git://anonscm.debian.org/debian-med/bamtools.git


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