From 7fb6a7b1826a73ecfcf8815d9c4e0e89c197e93c Mon Sep 17 00:00:00 2001 From: Neil Blakey-Milner Date: Thu, 27 Jul 2000 14:33:00 +0000 Subject: Add sim4, an implementation of the sim4 algorithm for aligning expressed DNA with genomic sequences PR: ports/20219 Submitted by: Johann Visagie --- biology/Makefile | 1 + biology/sim4/Makefile | 23 +++++++++++++++++++++++ biology/sim4/distinfo | 1 + biology/sim4/files/patch-aa | 10 ++++++++++ biology/sim4/pkg-comment | 1 + biology/sim4/pkg-descr | 11 +++++++++++ biology/sim4/pkg-plist | 1 + 7 files changed, 48 insertions(+) create mode 100644 biology/sim4/Makefile create mode 100644 biology/sim4/distinfo create mode 100644 biology/sim4/files/patch-aa create mode 100644 biology/sim4/pkg-comment create mode 100644 biology/sim4/pkg-descr create mode 100644 biology/sim4/pkg-plist (limited to 'biology') 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 +# +# $FreeBSD$ +# + +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 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 -- cgit v1.2.3