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.
Thanks.
> > 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
Andreas.
--
http://fam-tille.de
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