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
