Re: BLAST+ speed & build issues
[Sorry for the belated reply; I was on vacation when this thread started
and have only just caught up to it.]
Tim Booth <avarus@fastmail.fm> writes:
> These don't break the build but they should really be disabled. Is
> there an easy way to do this, do you think?
Yes, just comment out the relevant per-project makefiles' CHECK_CMD settings.
> A user reported that his analysis took an order of magnitude longer
> after upgrading BLAST+ (from the static binary build to the Debian Med
> build). I'd expect some slowdown with dynamic linking but this is
> indeed fairly drastic:
Dynamic linking does indeed add a fair bit of startup overhead. :-/
OTOH, the BLAST+ executables support input files containing multiple
queries, which should reduce its impact (but may entail reworking some
scripts).
> If the latter, I know the real fix is for script authors use BLAST more
> sensibly, but I'm wondering if there is any mileage in trying to make a
> ncbi-blast+-static package?
That's an interesting idea, but it would probably be pretty hefty. As
far as logistics go, I'd suggest that it provide/conflict/replace
ncbi-blast+ (and ship separate copies of its handful of
architecture-independent files) rather than pretending to be
coinstallable.
--
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu
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