Hi Andreas, >>> 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.
Thanks! Let's hope I will be able to upload updates by myself when it hits the archive ;) >>> 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" > ... Maybe we should... unless the repo you linked above is indeed 'the free SSPACE version'. I noticed it said 'SSPACE basic' while the Baseclear link below read 'SSPACE standard' -- so maybe there's a functionality delta between the free and non-free versions that makes all the difference. >>> 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? I can see to it, but have other things on my agenda atm. It's on my list now though :) Best wishes 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.