From johann@sanbi.ac.za  Thu Jul 27 07:00:57 2000
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Date: Thu, 27 Jul 2000 16:00:48 +0200
From: johann@egenetics.com
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To: FreeBSD-gnats-submit@freebsd.org
Subject: New port: biology/sim4
X-Send-Pr-Version: 3.2

>Number:         20219
>Category:       ports
>Synopsis:       New port: biology/sim4
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Thu Jul 27 07:10:00 PDT 2000
>Closed-Date:    Thu Jul 27 07:33:08 PDT 2000
>Last-Modified:  Thu Jul 27 07:33:52 PDT 2000
>Originator:     Johann Visagie
>Release:        FreeBSD 3.5-STABLE i386
>Organization:
Electric Genetics
>Environment:
FreeBSD fling.sanbi.ac.za 3.5-STABLE FreeBSD 3.5-STABLE #2: Fri Jul 14 17:30:00 SAST 2000     toor@fling.sanbi.ac.za:/usr/src/sys/compile/FLING i386
>Description:
New port of a tool implementing the sim4 gene alignment algorithm
>How-To-Repeat:
N/A
>Fix:
# 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:
#
#	sim4
#	sim4/pkg
#	sim4/pkg/PLIST
#	sim4/pkg/DESCR
#	sim4/pkg/COMMENT
#	sim4/patches
#	sim4/patches/patch-aa
#	sim4/Makefile
#	sim4/files
#	sim4/files/md5
#
echo c - sim4
mkdir -p sim4 > /dev/null 2>&1
echo c - sim4/pkg
mkdir -p sim4/pkg > /dev/null 2>&1
echo x - sim4/pkg/PLIST
sed 's/^X//' >sim4/pkg/PLIST << 'END-of-sim4/pkg/PLIST'
Xbin/sim4
END-of-sim4/pkg/PLIST
echo x - sim4/pkg/DESCR
sed 's/^X//' >sim4/pkg/DESCR << 'END-of-sim4/pkg/DESCR'
XThis package implements the Sim4 algorithm for aligning expressed DNA
Xwith genomic sequences, described in the paper:
X
XL. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998)
X"A computer program for aligning a cDNA sequence with a genomic DNA sequence."
XGenome Research 8, 967-974.
X
XWWW: http://globin.cse.psu.edu/
X
X- Johann
Xjohann@egenetics.com
END-of-sim4/pkg/DESCR
echo x - sim4/pkg/COMMENT
sed 's/^X//' >sim4/pkg/COMMENT << 'END-of-sim4/pkg/COMMENT'
XAn algorithm for aligning expressed DNA with genomic sequences
END-of-sim4/pkg/COMMENT
echo c - sim4/patches
mkdir -p sim4/patches > /dev/null 2>&1
echo x - sim4/patches/patch-aa
sed 's/^X//' >sim4/patches/patch-aa << 'END-of-sim4/patches/patch-aa'
X--- Makefile.orig	Thu Jul 13 21:09:47 2000
X+++ Makefile	Thu Jul 27 15:44:17 2000
X@@ -4,7 +4,9 @@
X # For Sun's compilers under Solaris, ``-fast'' works well.
X # For gcc, ``-O2'' works well.
X 
X+CFLAGS+= -O2
X+
X sim4:
X-	cc -o sim4 -I. -O *.c -lm
X+	cc -o sim4 -I. ${CFLAGS} *.c -lm
X clean:
X 	rm -f sim4 *.o
END-of-sim4/patches/patch-aa
echo x - sim4/Makefile
sed 's/^X//' >sim4/Makefile << 'END-of-sim4/Makefile'
X# New ports collection makefile for:	sim4
X# Date created:		27 July 2000
X# Whom:	      		Johann Visagie <johann@egenetics.com>
X#
X# $FreeBSD$
X#
X
XPORTNAME=	sim4
XPORTVERSION=	2000.07.13
XCATEGORIES=	biology
XMASTER_SITES=	http://globin.cse.psu.edu/ftp/dist/sim4/
XDISTNAME=	sim4
X
XMAINTAINER=	johann@egenetics.com
X
XWRKSRC=		${WRKDIR}/sim4.2000-07-13
X
XALL_TARGET=	sim4
X
Xdo-install:
X	@ ${INSTALL_PROGRAM} ${WRKSRC}/sim4 ${PREFIX}/bin
X
X.include <bsd.port.mk>
END-of-sim4/Makefile
echo c - sim4/files
mkdir -p sim4/files > /dev/null 2>&1
echo x - sim4/files/md5
sed 's/^X//' >sim4/files/md5 << 'END-of-sim4/files/md5'
XMD5 (sim4.tar.gz) = aad9ecab4978424fb6ec6cd60140f948
END-of-sim4/files/md5
exit


>Release-Note:
>Audit-Trail:
State-Changed-From-To: open->closed 
State-Changed-By: nbm 
State-Changed-When: Thu Jul 27 07:33:08 PDT 2000 
State-Changed-Why:  
Added, thanks! (: 

http://www.freebsd.org/cgi/query-pr.cgi?pr=20219 
>Unformatted:
