Date: Sun, 28 Dec 2014 13:08:17 -0600 From: Jason Bacon <jwbacon@tds.net> To: =?UTF-8?B?RGFnLUVybGluZyBTbcO4cmdyYXY=?= <des@des.no>, John Marino <marino@FreeBSD.org> Cc: svn-ports-head@freebsd.org, svn-ports-all@freebsd.org, ports-committers@freebsd.org Subject: Re: svn commit: r370220 - in head/biology: . ncbi-blast Message-ID: <54A05521.7010302@tds.net> In-Reply-To: <86r3vjg054.fsf@nine.des.no> References: <201410062016.s96KGZP8084850@svn.freebsd.org> <86r3vjg054.fsf@nine.des.no>
next in thread | previous in thread | raw e-mail | index | archive | help
Actually, there are many implementations of the BLAST algorithms, but this implementation of BLAST+ is the only one undergoing continued development at NCBI, so I'm not sure why you think there's a problem with calling the port ncbi-blast. The legacy NCBI blast is already available in biology/ncbi-toolkit and can remain there for applications that need it. Other blast implementations should have a prefix other than ncbi-. See: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download Regards, JB On 12/28/14 11:22 AM, 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. > > DES -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jason W. Bacon jwbacon@tds.net Circumstances don't make a man: They reveal him. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?54A05521.7010302>