Re: blast+ packaging
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
>>
>>
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