Hi, thanks for the info. Regarding binaries size vs compiled from source, I know that by default, compilation is done with debug enabled, and increase size/lower performance.
For uscan I did not have a look yet, for the moment I will try to get compilation done... The legacy_blast.pl is given in the source code. I will have a look at alternatives when basic compile/install is ok. Olivier Le 4/27/11 4:32 PM, Tim Booth a écrit : > Hi Olivier, > > This was on my RADAR but I'm currently about to tackle AmplicoNoise > (must remember to file an ITP before I start...) so please go ahead. I > had a look at it at the sprint and this is what I found: > > 1) This may have been down to our rubbish wireless link but there > appeared to be something stopping automated downloads (ie. Uscan) from > NCBI. I know they do have anti-leeching on some of their sites. Do you > get any problems? > > 2) The current blast2 package has a version that tallies with the blast+ > version - ie. 1:2.2.24.20100808-2, yet the blast2 package doesn't > contain Blast+ and I can't see where this version is coming from in > blast2 given that it is built from the NCBI C toolkit which is versioned > by date. I started to look into this and ran out of time - any idea? > > 3) There is a handy script called legacy_blast.pl that emulates blastall > and thus allows BLAST+ to be used with tools like T-Coffee. I can't > remember if this is in the upstream tarball or not, but if so it might > be worth using the alternatives system to allow BLAST+ to fill in for > legacy BLAST. > > 4) The BLAST+ binaries, if downloaded pre-compiled from NCBI, come in at > a whopping great size compared to the source code. I was meaning to > look into what was going on (muchos static linking??) but never got > around to it. > > 5) There should be a default $BLASTDB directory, I think. Can't > remember what the Debian policy is on apps that need a certain > environment set before they will run but I'm sure the basic idea is to > try and set defaults so the app will run out-of-the-box. > > Anyway, I gather BLAST+ should be less of a beast to package then the > original, so have fun. I'm not very good at reading the list so if you > are able to CC me on any messages that would be appreciated. > > Cheers, > > TIM > > On Wed, 2011-04-27 at 14:53 +0200, Andreas Tille wrote: >> Hi Olivier, >> >> On Wed, Apr 27, 2011 at 02:35:55PM +0200, Olivier Sallou wrote: >>> Has anyone started something? Or should I go for it ? >> If you are brave enough to tackle this there are several people who >> would be happy about this (and some other programs depend from it. >> >> I would strongly advise to CC Aaron Ucko (as I did now) because he is >> the ncbi / blast expert and I think I remember he had given some >> statement about blast+. While Aaron is a member of the Debian Med team >> he does not follow this list strictly - so CCing him makes sense. >> >> Kind regards >> >> Andreas. >> >> -- >> http://fam-tille.de >> >> -- gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
