Re: blast+ packaging
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
>
>
--
To Err is human.
To Arrr is Pirate!
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