Attachment 98045 Details for Bug 136877 – file.shar

file.shar

file.shar (text/plain), 3.49 KB, created by Ben Allen on 2009-07-17 22:20:01 UTC

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Creator: Ben Allen

Created: 2009-07-17 22:20:01 UTC

Size: 3.49 KB

patch

obsolete

># 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

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Attachments on bug 136877: 98045 | 98046