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>

6 files changed, 85 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index b998d56847c..bf13346a0bf 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -89,6 +89,7 @@
     SUBDIR += seqio
     SUBDIR += seqtools
     SUBDIR += sim4
+    SUBDIR += slclust
     SUBDIR += ssaha
     SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
diff --git a/biology/slclust/Makefile b/biology/slclust/Makefile
new file mode 100644
index 00000000000..628a08d0102
--- /dev/null
+++ b/biology/slclust/Makefile
@@ -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>
diff --git a/biology/slclust/distinfo b/biology/slclust/distinfo
new file mode 100644
index 00000000000..697a2f41840
--- /dev/null
+++ b/biology/slclust/distinfo
@@ -0,0 +1,2 @@
+SHA256 (slclust_02022010.tar.gz) = 9e21b65288e7fc35647721380cfedffd68608e164b4240c692c511c18c1620f8
+SIZE (slclust_02022010.tar.gz) = 23097
diff --git a/biology/slclust/files/patch-include_cmd__line__opts.h b/biology/slclust/files/patch-include_cmd__line__opts.h
new file mode 100644
index 00000000000..7b07b07ce28
--- /dev/null
+++ b/biology/slclust/files/patch-include_cmd__line__opts.h
@@ -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);
diff --git a/biology/slclust/files/patch-src_Makefile b/biology/slclust/files/patch-src_Makefile
new file mode 100644
index 00000000000..cee6db5e3a0
--- /dev/null
+++ b/biology/slclust/files/patch-src_Makefile
@@ -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}
+ 
diff --git a/biology/slclust/pkg-descr b/biology/slclust/pkg-descr
new file mode 100644
index 00000000000..74d667f5afa
--- /dev/null
+++ b/biology/slclust/pkg-descr
@@ -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/