Date: Fri, 17 Jul 2009 21:15:51 GMT From: Ben Allen <ben@sysadminschronicles.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/136877: New Port: biology/phyml A simple, fast, and accurate algorithm to estimate large phylogenies Message-ID: <200907172115.n6HLFpQm044225@www.freebsd.org> Resent-Message-ID: <200907172120.n6HLK1lx011168@freefall.freebsd.org>
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>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 <bsd.port.mk>
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:
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