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From: =?utf-8?Q?Dag-Erling_Sm=C3=B8rgrav?= <des@des.no>
To: John Marino <marino@FreeBSD.org>
Subject: Re: svn commit: r370220 - in head/biology: . ncbi-blast
References: <201410062016.s96KGZP8084850@svn.freebsd.org>
Date: Sun, 28 Dec 2014 18:22:15 +0100
In-Reply-To: <201410062016.s96KGZP8084850@svn.freebsd.org> (John Marino's
 message of "Mon, 6 Oct 2014 20:16:35 +0000 (UTC)")
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John Marino <marino@FreeBSD.org> writes:
> Log:
>   Add new port biology/ncbi-blast
>=20=20=20
>   PR:		190854
>   Submitted by:	Jason Bacon
>=20=20=20
>   The Basic Local Alignment Search Tool (BLAST) finds regions of local
>   similarity between sequences. The program compares nucleotide or protein
>   sequences to sequence databases and calculates the statistical
>   significance of matches. BLAST can be used to infer functional and
>   evolutionary relationships between sequences as well as help identify
>   members of gene families.

I wish I had caught this in time.

This is wrong.  The port you committed installs BLAST+, not BLAST.
These are two significantly different programs which implement the same
algorithm.  While the former is intended as a successor to the latter,
they are not interchangeable.  Many applications which use BLAST have
not yet been, and may never be, ported to BLAST+, and this port stands
in the way of a BLAST port.

Since the authors, in their infinite stup^H^H^H^Hwisdom, decided to
start numbering BLAST+ versions where BLAST left off, there is no way to
fix this without either a) bumping PORTEPOCH or b) naming the BLAST port
blast-legacy or something similar, while renaming this one to blast+ or
blast-plus.

DES
--=20
Dag-Erling Sm=C3=B8rgrav - des@des.no