Attachment 82846 Details for Bug 118460 – file.shar

file.shar

file.shar (text/plain), 7.38 KB, created by Motomichi Matsuzaki on 2007-12-06 12:40:01 UTC

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Creator: Motomichi Matsuzaki

Created: 2007-12-06 12:40:01 UTC

Size: 7.38 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:
>#
>#	biology/muscle/
>#	biology/muscle/Makefile
>#	biology/muscle/distinfo
>#	biology/muscle/files
>#	biology/muscle/files/patch-Makefile
>#	biology/muscle/files/patch-intmath.cpp
>#	biology/muscle/files/patch-globalslinux.cpp
>#	biology/muscle/pkg-descr
>#
>echo c - biology/muscle/
>mkdir -p biology/muscle/ > /dev/null 2>&1
>echo x - biology/muscle/Makefile
>sed 's/^X//' >biology/muscle/Makefile << 'END-of-biology/muscle/Makefile'
>X# New ports collection makefile for:	muscle
>X# Date created:	6 December 2007
>X# Whom:		Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
>X#
>X# $FreeBSD$
>X#
>X
>XPORTNAME=	muscle
>XPORTVERSION=	3.6
>XCATEGORIES=	biology
>XMASTER_SITES=	http://www.drive5.com/muscle/downloads${PORTVERSION}/
>XDISTNAME=	${PORTNAME}${PORTVERSION}_src
>X
>X.if !defined(NOPORTDOCS)
>XEXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
>XDISTFILES=	${EXTRACT_ONLY}
>XPORTDOCS=	${PORTNAME}.pdf ${PORTNAME}.html
>XMASTER_SITES+=	http://www.drive5.com/muscle/:docs
>X.for file in ${PORTDOCS}
>XDISTFILES+=	${file}:docs
>X.endfor
>X.endif
>X
>XMAINTAINER=	mzaki@biol.s.u-tokyo.ac.jp
>XCOMMENT=	MUltiple Sequence Comparison by Log-Expectation
>X
>XUSE_GMAKE=	yes
>X
>XPLIST_FILES=	bin/muscle
>X
>Xdo-install:
>X	${INSTALL_PROGRAM} ${WRKSRC}/muscle ${PREFIX}/bin
>X.if !defined(NOPORTDOCS)
>X	@${MKDIR} ${DOCSDIR}
>X.for file in ${PORTDOCS}
>X	@${INSTALL_DATA} ${DISTDIR}/${file} ${DOCSDIR}
>X.endfor
>X.endif
>X
>X.include <bsd.port.mk>
>END-of-biology/muscle/Makefile
>echo x - biology/muscle/distinfo
>sed 's/^X//' >biology/muscle/distinfo << 'END-of-biology/muscle/distinfo'
>XMD5 (muscle3.6_src.tar.gz) = e721d0859da9feec3cedeb42dcee9f59
>XSHA256 (muscle3.6_src.tar.gz) = 32b818a51f421e1d687f513dc31374a330470950151a5e7df961e64781699431
>XSIZE (muscle3.6_src.tar.gz) = 185267
>XMD5 (muscle.pdf) = de726534562fccec33bb75ec664ec0d5
>XSHA256 (muscle.pdf) = a28fd0afc0919c176a9a1cedb3b46cadb24a53c575089305cc4b2967ec4a5fc9
>XSIZE (muscle.pdf) = 239031
>XMD5 (muscle.html) = 9db61f19113786e0a181c3218c382d7b
>XSHA256 (muscle.html) = 4df43445f08d99e18da71a06438cc8fc3ba42b6709e19c8cfea0c31788dc17b6
>XSIZE (muscle.html) = 94645
>END-of-biology/muscle/distinfo
>echo c - biology/muscle/files
>mkdir -p biology/muscle/files > /dev/null 2>&1
>echo x - biology/muscle/files/patch-Makefile
>sed 's/^X//' >biology/muscle/files/patch-Makefile << 'END-of-biology/muscle/files/patch-Makefile'
>X--- Makefile.orig	Fri Sep  9 07:26:04 2005
>X+++ Makefile	Tue Dec 20 18:50:33 2005
>X@@ -9,28 +9,14 @@
>X # On OSX, using -static gives the error "ld: can't locate file for: -lcrt0.o",
>X # this is fixed by deleting "-static" from the LDLIBS line.
>X 
>X-CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1
>X-LDLIBS = -lm -static
>X-# LDLIBS = -lm
>X-
>X-OBJ = .o
>X-EXE =
>X-
>X-RM = rm -f
>X-CP = cp
>X-
>X-GPP = g++
>X-LD = $(GPP) $(CFLAGS)
>X-CPP = $(GPP) -c $(CFLAGS) 
>X+CC = g++
>X+CXXFLAGS += -O3 -funroll-loops -Winline -DNDEBUG=1
>X+LDLIBS = -lm -lkvm
>X 
>X all: muscle
>X 
>X CPPSRC = $(sort $(wildcard *.cpp))
>X CPPOBJ	= $(subst .cpp,.o,$(CPPSRC))
>X 
>X-$(CPPOBJ): %.o: %.cpp
>X-	$(CPP) $< -o $@
>X-
>X muscle: $(CPPOBJ)
>X-	$(LD) -o muscle $(CPPOBJ) $(LDLIBS)
>X-	strip muscle
>X+	$(LINK.o) -o $@ $^ $(LDLIBS)
>END-of-biology/muscle/files/patch-Makefile
>echo x - biology/muscle/files/patch-intmath.cpp
>sed 's/^X//' >biology/muscle/files/patch-intmath.cpp << 'END-of-biology/muscle/files/patch-intmath.cpp'
>X--- intmath.cpp.orig	Tue Nov 30 05:09:50 2004
>X+++ intmath.cpp	Mon Jul  4 07:49:45 2005
>X@@ -8,13 +8,6 @@
>X 	return (PROB) pow(2.0, (double) Score/INTSCALE);
>X 	}
>X 
>X-static const double log2e = log2(exp(1.0));
>X-
>X-double lnTolog2(double ln)
>X-	{
>X-	return ln*log2e;
>X-	}
>X-
>X double log2(double x)
>X 	{
>X 	if (0 == x)
>X@@ -24,6 +17,13 @@
>X // Multiply by inverse of log(2) just in case multiplication
>X // is faster than division.
>X 	return log(x)*dInvLn2;
>X+	}
>X+
>X+static const double log2e = log2(exp(1.0));
>X+
>X+double lnTolog2(double ln)
>X+	{
>X+	return ln*log2e;
>X 	}
>X 
>X SCORE ProbToScore(PROB Prob)
>END-of-biology/muscle/files/patch-intmath.cpp
>echo x - biology/muscle/files/patch-globalslinux.cpp
>sed 's/^X//' >biology/muscle/files/patch-globalslinux.cpp << 'END-of-biology/muscle/files/patch-globalslinux.cpp'
>X--- globalslinux.cpp.orig	Tue Nov 30 05:09:50 2004
>X+++ globalslinux.cpp	Mon Jul  4 11:13:18 2005
>X@@ -7,6 +7,12 @@
>X #include <errno.h>
>X #include <stdio.h>
>X #include <fcntl.h>
>X+#if __FreeBSD__ > 2
>X+#include <kvm.h>
>X+#include <sys/param.h>
>X+#include <sys/sysctl.h>
>X+#include <sys/user.h>
>X+#endif // __FreeBSD__ > 2
>X 
>X const int ONE_MB = 1000000;
>X const int MEM_WARNING_THRESHOLD = 20*ONE_MB;
>X@@ -39,6 +45,34 @@
>X 	return szCmdLine;
>X 	}
>X 
>X+#if __FreeBSD__ > 2
>X+double GetMemUseMB()
>X+	{
>X+	kvm_t *kd;
>X+	struct kinfo_proc *ki;
>X+	vm_size_t size;
>X+	int nproc;
>X+
>X+	kd = kvm_open(NULL, "/dev/null", NULL, O_RDONLY, "kvm_open");
>X+	if (kd == NULL)
>X+		{
>X+		static bool Warned = false;
>X+		if (!Warned)
>X+			{
>X+			Warned = true;
>X+			Warning("*Warning* Cannot open KVM");
>X+			}
>X+		return 0;
>X+		}
>X+
>X+	ki = kvm_getprocs(kd, KERN_PROC_PID, getpid(), &nproc);
>X+	size = ki->ki_size;
>X+
>X+	kvm_close(kd);
>X+
>X+	return ((double) size)/1e6;
>X+	}
>X+#else // __FreeBSD__ > 2
>X double GetMemUseMB()
>X 	{
>X 	static char statm[64];
>X@@ -83,6 +117,7 @@
>X 
>X 	return ((double) Pages * (double) PageSize)/1e6;
>X 	}
>X+#endif // __FreeBSD__ > 2
>X 
>X void SaveCmdLine(int argc, char *argv[])
>X 	{
>X@@ -118,6 +153,28 @@
>X 		dPeakMemUseMB = dMB;
>X 	}
>X 
>X+#if __FreeBSD__ > 2
>X+double GetRAMSizeMB()
>X+	{
>X+	const double DEFAULT_RAM = 500;
>X+	unsigned int physmem;
>X+	size_t len = sizeof physmem;
>X+	static int mib[2] = { CTL_HW, HW_PHYSMEM };
>X+
>X+	if (sysctl(mib, 2, &physmem, &len, NULL, 0))
>X+		{
>X+		static bool Warned = false;
>X+		if (!Warned)
>X+			{
>X+			Warned = true;
>X+			Warning("*Warning* Cannot get hw.physmem");
>X+			}
>X+		return DEFAULT_RAM;
>X+		}
>X+
>X+	return ((double) physmem)/1e6;
>X+	}
>X+#else // __FreeBSD__ > 2
>X double GetRAMSizeMB()
>X 	{
>X 	const double DEFAULT_RAM = 500;
>X@@ -168,5 +225,6 @@
>X 	int Bytes = atoi(pMem+9)*1000;
>X 	return ((double) Bytes)/1e6;
>X 	}
>X+#endif // __FreeBSD__ > 2
>X 
>X #endif	// !WIN32
>END-of-biology/muscle/files/patch-globalslinux.cpp
>echo x - biology/muscle/pkg-descr
>sed 's/^X//' >biology/muscle/pkg-descr << 'END-of-biology/muscle/pkg-descr'
>XMUSCLE is multiple alignment software for protein and nucleotide sequences.
>XThe name stands for multiple sequence comparison by log-expectation.
>X
>XA range of options is provided that give you the choice of optimizing
>Xaccuracy, speed, or some compromise between the two. Default parameters are
>Xthose that give the best average accuracy in the published tests. MUSCLE
>Xcan achieve both better average accuracy and better speed than CLUSTALW or
>XT-Coffee, depending on the chosen options.
>X
>XCitation:
>X
>XEdgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
>Xand high throughput. Nucleic Acids Research 32(5): 1792-1797. 
>X
>XEdgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
>Xreduced time and space complexity. BMC Bioinformatics 5(1): 113. 
>X
>XThe NAR paper gives only a brief overview of the algorithm and
>Ximplementation details. For a full discussion of the method and many of
>Xthe non-default options that it offers, please see the BMC paper.
>X
>XWWW: http://www.drive5.com/muscle/
>END-of-biology/muscle/pkg-descr
>exit

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Attachments on bug 118460: 82846