Re: RFS: ariba

[Sascha Steinbiss <sascha@steinbiss.name>]

Hi Andreas,

thanks for having a look at the package.

> when building I see several lines like
> 
> 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.

> 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).

> 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).

Kind regards
Sascha


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