Date: Wed, 23 Mar 2016 11:00:44 +0000 (UTC) From: Raphael Kubo da Costa <rakuco@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r411697 - in head/biology: . slclust slclust/files Message-ID: <201603231100.u2NB0i8d016421@repo.freebsd.org>
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Author: rakuco Date: Wed Mar 23 11:00:44 2016 New Revision: 411697 URL: https://svnweb.freebsd.org/changeset/ports/411697 Log: New port: biology/slclust. Slclust is a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. WWW: http://sourceforge.net/projects/slclust/ PR: 207997 Submitted by: Jason Bacon <bacon4000@gmail.com> Added: head/biology/slclust/ head/biology/slclust/Makefile (contents, props changed) head/biology/slclust/distinfo (contents, props changed) head/biology/slclust/files/ head/biology/slclust/files/patch-include_cmd__line__opts.h (contents, props changed) head/biology/slclust/files/patch-src_Makefile (contents, props changed) head/biology/slclust/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Wed Mar 23 10:57:42 2016 (r411696) +++ head/biology/Makefile Wed Mar 23 11:00:44 2016 (r411697) @@ -89,6 +89,7 @@ SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 + SUBDIR += slclust SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee Added: head/biology/slclust/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/slclust/Makefile Wed Mar 23 11:00:44 2016 (r411697) @@ -0,0 +1,23 @@ +# Created by: Jason Bacon <bacon4000@gmail.com> +# $FreeBSD$ + +PORTNAME= slclust +PORTVERSION= 2010.02.02 +CATEGORIES= biology +MASTER_SITES= SF +MASTER_SITE_SUBDIR= slclust/slclust +DISTNAME= ${PORTNAME}_02022010 + +MAINTAINER= bacon4000@gmail.com +COMMENT= Single-linkage clustering with Jaccard similarity + +LICENSE= ART10 + +WRKSRC= ${WRKDIR}/${PORTNAME} + +PLIST_FILES= bin/slclust + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/src/slclust ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/biology/slclust/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/slclust/distinfo Wed Mar 23 11:00:44 2016 (r411697) @@ -0,0 +1,2 @@ +SHA256 (slclust_02022010.tar.gz) = 9e21b65288e7fc35647721380cfedffd68608e164b4240c692c511c18c1620f8 +SIZE (slclust_02022010.tar.gz) = 23097 Added: head/biology/slclust/files/patch-include_cmd__line__opts.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/slclust/files/patch-include_cmd__line__opts.h Wed Mar 23 11:00:44 2016 (r411697) @@ -0,0 +1,9 @@ +--- include/cmd_line_opts.h.orig 2010-02-02 14:00:41 UTC ++++ include/cmd_line_opts.h +@@ -1,5 +1,5 @@ + #ifndef __CMD_LINE_OPTS_H__ +-#define __CMD_LiNE_OPTS_H__ ++#define __CMD_LINE_OPTS_H__ + + bool co_get_int(int argc, char** argv, const char* text, int* ); + bool co_get_bool(int argc, char** argv, const char* text); Added: head/biology/slclust/files/patch-src_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/slclust/files/patch-src_Makefile Wed Mar 23 11:00:44 2016 (r411697) @@ -0,0 +1,45 @@ +--- src/Makefile.orig 2010-02-02 14:00:41 UTC ++++ src/Makefile +@@ -20,8 +20,8 @@ LIBS = + # How they are invoked on the compile line (eg: -lspecial) + LLIBS = + +-# Local additions for the CFLAG options +-LOCAL_CFLAGS = -Wall ++# Local additions for the CXXFLAGS options ++#LOCAL_CXXFLAGS = -Wall + #-static + + +@@ -34,8 +34,8 @@ BIN = ${PROJECT_ROOT}/bin + INCLUDE = ${PROJECT_ROOT}/include + + DEBUG = DEBUG +-CFLAGS = -I${INCLUDE} ${LOCAL_CFLAGS} +-CC = g++ ${CFLAGS} ++CXXFLAGS += -I${INCLUDE} ${LOCAL_CXXFLAGS} ++CXX ?= g++ + + MAKEFILE = Makefile + +@@ -43,10 +43,10 @@ MAKEFILE = Makefile + # Suffix rules + + .cc.o: +- ${CC} -c $< ++ ${CXX} -c ${CXXFLAGS} $< + + .cpp.o: +- ${CC} -c $< ++ ${CXX} -c ${CXXFLAGS} $< + + # Target dependencies + +@@ -65,6 +65,6 @@ clean : + ${OBJ} : ${MAKEFILE} + + ${EXECUTABLE} : ${OBJS} +- ${CC} ${OBJS} ${LIBS} -o ${EXECUTABLE} ++ ${CXX} ${OBJS} ${LIBS} -o ${EXECUTABLE} + chmod 755 ${EXECUTABLE} + Added: head/biology/slclust/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/slclust/pkg-descr Wed Mar 23 11:00:44 2016 (r411697) @@ -0,0 +1,5 @@ +Slclust is a utility that performs single-linkage clustering with the option of +applying a Jaccard similarity coefficient to break weakly bound clusters into +distinct clusters. + +WWW: http://sourceforge.net/projects/slclust/
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