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Re: SPAdes for Debian

Hi Anton,

just to let you know that we are working on this.

On Wed, Apr 02, 2014 at 02:51:32PM +0400, Anton Korobeynikov wrote:
> >> 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
> > false?
> We will see what can be done here. Right now there will be non-zero
> return code in case of any crash. But we'll also check the results.

> > Hmmm, could you please be more verbose about this.
> Here it is: https://github.com/iontorrent/bamtools

I noticed that some preparation for packaging was done in the past but
stalled for unknown reason.  I updated the packaging to the latest
version but was running into some issues I need to sort out first.

> >  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?
> Well, I do not know all the differences, in fact. We prefer to use
> IonTorrent version because we know it's used in TorrentSuite and we
> tend to play safe wrt (possible) incompatibilities :)

Before I'll upload I'll do some investigation into this to check the
difference.  If it seems to be relevant - specifically to fit the needs
for SPAdes without harming other compatibility - we might decide for
this version as well.  I would even try to contact both upstreams
whether they might intent to merge their effort.

Thanks for the hints



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