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 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
