7 files changed, 48 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index f0b43f8b45c3..d91b479913aa 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -18,6 +18,7 @@
     SUBDIR += psi88
     SUBDIR += rasmol
     SUBDIR += seaview
+    SUBDIR += sim4
     SUBDIR += tinker
     SUBDIR += xdrawchem
     SUBDIR += xmolwt
diff --git a/biology/sim4/Makefile b/biology/sim4/Makefile
new file mode 100644
index 000000000000..a988b24558ab
--- /dev/null
+++ b/biology/sim4/Makefile
@@ -0,0 +1,23 @@
+# New ports collection makefile for:	sim4
+# Date created:		27 July 2000
+# Whom:	      		Johann Visagie <johann@egenetics.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	sim4
+PORTVERSION=	2000.07.13
+CATEGORIES=	biology
+MASTER_SITES=	http://globin.cse.psu.edu/ftp/dist/sim4/
+DISTNAME=	sim4
+
+MAINTAINER=	johann@egenetics.com
+
+WRKSRC=		${WRKDIR}/sim4.2000-07-13
+
+ALL_TARGET=	sim4
+
+do-install:
+	@ ${INSTALL_PROGRAM} ${WRKSRC}/sim4 ${PREFIX}/bin
+
+.include <bsd.port.mk>
diff --git a/biology/sim4/distinfo b/biology/sim4/distinfo
new file mode 100644
index 000000000000..ac470bbbaf67
--- /dev/null
+++ b/biology/sim4/distinfo
@@ -0,0 +1 @@
+MD5 (sim4.tar.gz) = aad9ecab4978424fb6ec6cd60140f948
diff --git a/biology/sim4/files/patch-aa b/biology/sim4/files/patch-aa
new file mode 100644
index 000000000000..83a5316370e9
--- /dev/null
+++ b/biology/sim4/files/patch-aa
@@ -0,0 +1,10 @@
+--- Makefile.orig	Thu Jul 13 12:09:47 2000
++++ Makefile	Thu Jul 27 07:28:18 2000
+@@ -5,6 +5,6 @@
+ # For gcc, ``-O2'' works well.
+ 
+ sim4:
+-	cc -o sim4 -I. -O *.c -lm
++	${CC} -o sim4 -I. ${CFLAGS} *.c -lm
+ clean:
+ 	rm -f sim4 *.o
diff --git a/biology/sim4/pkg-comment b/biology/sim4/pkg-comment
new file mode 100644
index 000000000000..7e50b5e0e13f
--- /dev/null
+++ b/biology/sim4/pkg-comment
@@ -0,0 +1 @@
+An algorithm for aligning expressed DNA with genomic sequences
diff --git a/biology/sim4/pkg-descr b/biology/sim4/pkg-descr
new file mode 100644
index 000000000000..a5f4cdb174af
--- /dev/null
+++ b/biology/sim4/pkg-descr
@@ -0,0 +1,11 @@
+This package implements the Sim4 algorithm for aligning expressed DNA
+with genomic sequences, described in the paper:
+
+L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998)
+"A computer program for aligning a cDNA sequence with a genomic DNA sequence."
+Genome Research 8, 967-974.
+
+WWW: http://globin.cse.psu.edu/
+
+- Johann
+johann@egenetics.com
diff --git a/biology/sim4/pkg-plist b/biology/sim4/pkg-plist
new file mode 100644
index 000000000000..166054a68786
--- /dev/null
+++ b/biology/sim4/pkg-plist
@@ -0,0 +1 @@
+bin/sim4