Date: Sun, 28 Dec 2014 19:17:57 +0100 From: John Marino <freebsd.contact@marino.st> To: =?UTF-8?B?RGFnLUVybGluZyBTbcO4cmdyYXY=?= <des@des.no>, John Marino <marino@FreeBSD.org> Cc: svn-ports-head@freebsd.org, svn-ports-all@freebsd.org, jwbacon@tds.net, ports-committers@freebsd.org Subject: Re: svn commit: r370220 - in head/biology: . ncbi-blast Message-ID: <54A04955.3010601@marino.st> In-Reply-To: <86r3vjg054.fsf@nine.des.no> References: <201410062016.s96KGZP8084850@svn.freebsd.org> <86r3vjg054.fsf@nine.des.no>
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On 12/28/2014 18:22, Dag-Erling Smørgrav wrote: > John Marino <marino@FreeBSD.org> writes: >> Log: >> Add new port biology/ncbi-blast >> >> PR: 190854 >> Submitted by: Jason Bacon >> >> 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. It's a brand new port with a unique name. Why is "bumping PORTEPOCH" considered necessary? Why is the existence of this port blocking the introduction of a new BLAST port? AFAIK, this port was not claiming to be a drop-in replacement for the blast port that was removed; no dependencies of other ports changed to this port. It seems that all that is needs is to update the pkg-descr file to specify it's the blast+ implementation. John
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