SSPACE (Was: RFS: ariba)
Hi Sascha,
On Wed, Jun 01, 2016 at 01:45:35PM +0100, Sascha Steinbiss wrote:
> > WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl.
> > But it is optional so will be skipped during assembly
>
> Yes, I have talked to ARIBA upstream (we're conveniently sharing the
> same office) and this is fine to skip; it's not really clear whether
> using it leads to significant improvement of the results.
OK. I've uploaded ariba to new.
> > About two years ago I did some rudimentary packaging if what was at
> > that time available from
> > http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/
> > where it vanished now. I somehow missed to commit my work from this time
> > but I noticed that there is sspace 2.1.1 at
> >
> > https://github.com/nsoranzo/sspace_basic/releases
> >
> > which claims to be GPL
>
> After a quick talk with Martin I'd be careful to check that license and
> the repo's owner's affiliation with the SSPACE authors... from what we
> know SSPACE (owned by Baseclear) has never been free. That's why it was
> made optional in ARIBA in the first place, along with GapFiller (also
> not free, same situation).
I personally can not tell how important SSPACE and GapFiller might be
but may be we should send another "please free your software mail" ...
> > as well as sspace 3.0
> >
> > http://www.mybiosoftware.com/sspace-1-2-scaffolding-pre-assembled-contigs-paired-read-data.html
> >
> > which links to a download page for academic use only.
>
> Hmm, this should be the most recent resource:
> http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE
>
> > I wonder how important sspace would be for ariba packaging and
> > whether I should have a take at 2.1.1 with my current local files.
>
> As I said, it's not important and skipping it is fine and it has been
> discussed with ARIBA's upstream. If you want you can take a shot at
> SSPACE basic from that GitHub repo, but if it was me packaging it I
> would probably try to confirm the license as GPL with the original
> authors (Boetzer and Pirovano).
Hmmmm, since you are obviously pretty well informed could you assume it
would be you who intends to package the Github version and ask upstream
perhaps a better informed question than I could do?
This would be really helpful.
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: