From owner-svn-ports-all@FreeBSD.ORG Sun Dec 28 19:08:27 2014 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 696222E1 for ; Sun, 28 Dec 2014 19:08:27 +0000 (UTC) Received: from mail-ie0-f173.google.com (mail-ie0-f173.google.com [209.85.223.173]) (using TLSv1 with cipher ECDHE-RSA-RC4-SHA (128/128 bits)) (Client CN "smtp.gmail.com", Issuer "Google Internet Authority G2" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 32B251172 for ; Sun, 28 Dec 2014 19:08:26 +0000 (UTC) Received: by mail-ie0-f173.google.com with SMTP id y20so11315630ier.4 for ; Sun, 28 Dec 2014 11:08:20 -0800 (PST) X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:message-id:date:from:user-agent:mime-version:to :cc:subject:references:in-reply-to:content-type :content-transfer-encoding; bh=0hAuGp6uIbsfTdqJde6V2dqevFPY6RGxiG0+ZhylAYY=; b=LMc9400Ae5ui2x1GUobdIu07lwwPV6IibWOu1eEi3/AFS+sdrEcsMoG+Su3ApUrQxD fCxzyvJRV6ndWxaQFqz+GX7GU5Q5rsop6RyY2TPkV4FEDMNnNZlW1G0nnwZKIhr9VnuN 7FK/M0T9+JiS4w+on+df/+ZVK1Dbi6CJADDiIpxTtq405fLPsnXtP5oMTnIdnr1VRQYV MH0fauqGW62ndxU99pGxLAHqe9FiHC9JAl+47Y9YWYhMcimC+q/o0IKJWqLaICYRK9Ac YWFt3UcGiuPNxlf407kQdz4V9ZW/uY7Y4e4NI+Ou+sBn3CexQlg5r5Hms6/W6W1hwUU2 9j7g== X-Gm-Message-State: ALoCoQkrVy9+Lfj2FxvFyfaoYoPxNtpGGPDdKzOMXXLsHoK6nywkWIx1pViIHhBTO4WKfsVcAJ4o X-Received: by 10.107.9.213 with SMTP id 82mr47064234ioj.45.1419793700208; Sun, 28 Dec 2014 11:08:20 -0800 (PST) Received: from [192.168.0.52] (h69-131-102-7.nwblwi.broadband.dynamic.tds.net. [69.131.102.7]) by mx.google.com with ESMTPSA id nm13sm13356253igb.5.2014.12.28.11.08.18 (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Sun, 28 Dec 2014 11:08:19 -0800 (PST) Message-ID: <54A05521.7010302@tds.net> Date: Sun, 28 Dec 2014 13:08:17 -0600 From: Jason Bacon User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:31.0) Gecko/20100101 Thunderbird/31.0 MIME-Version: 1.0 To: =?UTF-8?B?RGFnLUVybGluZyBTbcO4cmdyYXY=?= , John Marino Subject: Re: svn commit: r370220 - in head/biology: . ncbi-blast References: <201410062016.s96KGZP8084850@svn.freebsd.org> <86r3vjg054.fsf@nine.des.no> In-Reply-To: <86r3vjg054.fsf@nine.des.no> Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Cc: svn-ports-head@freebsd.org, svn-ports-all@freebsd.org, ports-committers@freebsd.org X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.18-1 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 28 Dec 2014 19:08:27 -0000 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 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. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~