From owner-freebsd-ports-bugs@FreeBSD.ORG Fri Jul 17 21:20:02 2009 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 2C643106566B for ; Fri, 17 Jul 2009 21:20:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 06B0E8FC1A for ; Fri, 17 Jul 2009 21:20:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.3/8.14.3) with ESMTP id n6HLK1Vo011169 for ; Fri, 17 Jul 2009 21:20:01 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id n6HLK1lx011168; Fri, 17 Jul 2009 21:20:01 GMT (envelope-from gnats) Resent-Date: Fri, 17 Jul 2009 21:20:01 GMT Resent-Message-Id: <200907172120.n6HLK1lx011168@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Ben Allen Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 9440B106564A for ; Fri, 17 Jul 2009 21:15:51 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [IPv6:2001:4f8:fff6::21]) by mx1.freebsd.org (Postfix) with ESMTP id 815F28FC1A for ; Fri, 17 Jul 2009 21:15:51 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.14.3/8.14.3) with ESMTP id n6HLFpX8044226 for ; Fri, 17 Jul 2009 21:15:51 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.14.3/8.14.3/Submit) id n6HLFpQm044225; Fri, 17 Jul 2009 21:15:51 GMT (envelope-from nobody) Message-Id: <200907172115.n6HLFpQm044225@www.freebsd.org> Date: Fri, 17 Jul 2009 21:15:51 GMT From: Ben Allen To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Cc: Subject: ports/136877: New Port: biology/phyml A simple, fast, and accurate algorithm to estimate large phylogenies X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 17 Jul 2009 21:20:02 -0000 >Number: 136877 >Category: ports >Synopsis: New Port: biology/phyml A simple, fast, and accurate algorithm to estimate large phylogenies >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Fri Jul 17 21:20:01 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Ben Allen >Release: 6.3 RELEASE >Organization: >Environment: FreeBSD ying 6.3-RELEASE-p7 FreeBSD 6.3-RELEASE-p7 #0: Sun Dec 21 03:24:04 UTC 2008 root@amd64-builder.daemonology.net:/usr/obj/usr/src/sys/SMP amd64 >Description: PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. >How-To-Repeat: >Fix: See attached shar. Patch attached with submission follows: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # phyml # phyml/Makefile # phyml/scripts # phyml/scripts/pre-configure # phyml/distinfo # phyml/pkg-descr # phyml/files # phyml/files/patch-src-configure.ac # echo c - phyml mkdir -p phyml > /dev/null 2>&1 echo x - phyml/Makefile sed 's/^X//' >phyml/Makefile << 'END-of-phyml/Makefile' X# New ports collection makefile for: phyml 3.0 20090706 X# Date created: July 17, 2009 X# Whom: ballen X# X# $FreeBSD$ X# X XPORTNAME= phyml XPORTVERSION= 20090706 XCATEGORIES= biology XMASTER_SITES= ${MASTER_SITE_GOOGLE_CODE} XDISTNAME= phyml_20090706 X XMAINTAINER= ben@sysadminschronicles.com XCOMMENT= A simple, fast, and accurate algorithm to estimate large phylogenies X XWRKSRC= ${WRKDIR}/${PORTNAME}/src XGNU_CONFIGURE= yes XPLIST_FILES= bin/phyml X X.include END-of-phyml/Makefile echo c - phyml/scripts mkdir -p phyml/scripts > /dev/null 2>&1 echo x - phyml/scripts/pre-configure sed 's/^X//' >phyml/scripts/pre-configure << 'END-of-phyml/scripts/pre-configure' Xcd ${WRKSRC} Xautoreconf Xchmod a+x install-sh Xrm missing Xautomake --add-missing END-of-phyml/scripts/pre-configure echo x - phyml/distinfo sed 's/^X//' >phyml/distinfo << 'END-of-phyml/distinfo' XMD5 (phyml_20090706.tar.gz) = 70e9963a04f5423124793467e8b50be0 XSHA256 (phyml_20090706.tar.gz) = b39fa8ba2bc3a6566f3463c77db0d8992f71a71af353be539d0916173785d4bd XSIZE (phyml_20090706.tar.gz) = 818229 END-of-phyml/distinfo echo x - phyml/pkg-descr sed 's/^X//' >phyml/pkg-descr << 'END-of-phyml/pkg-descr' XPhyML is a software that estimates maximum likelihood phylogenies from Xalignments of nucleotide or amino acid sequences. It provides a wide range of Xoptions that were designed to facilitate standard phylogenetic analyses. The Xmain strengths of PhyML lies in the large number of substitution models coupled Xto various options to search the space of phylogenetic tree topologies, going Xfrom very fast and efficient methods to slower but generally more accurate Xapproaches. It also implements two methods to evaluate branch supports in a Xsound statistical framework (the non-parametric bootstrap and the approximate Xlikelihood ratio test). PhyML was designed to process moderate to large data Xsets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long Xcan analyzed. In practice however, the amount of memory required to process a Xdata set is proportional of the product of the number of sequences by their Xlength. Hence, a large number of sequences can only be processed provided that Xthey are short. Also, PhyML can handle long sequences provided that they are Xnot numerous. With most standard personal computers, the "comfort zone" for XPhyML generally lies around 3 to 500 sequences less than 2,000 character long. END-of-phyml/pkg-descr echo c - phyml/files mkdir -p phyml/files > /dev/null 2>&1 echo x - phyml/files/patch-src-configure.ac sed 's/^X//' >phyml/files/patch-src-configure.ac << 'END-of-phyml/files/patch-src-configure.ac' X--- configure.ac.orig 2009-07-17 14:57:39.000000000 -0600 X+++ configure.ac 2009-07-17 14:57:55.000000000 -0600 X@@ -58,8 +58,6 @@ X esac X # End of cross-compilation macros X X-CFLAGS+=" -O3 -fomit-frame-pointer -funroll-loops -Wall" X- X AC_CONFIG_FILES([Makefile]) X AC_OUTPUT X END-of-phyml/files/patch-src-configure.ac exit >Release-Note: >Audit-Trail: >Unformatted: