Date: Thu, 27 Jul 2000 16:00:48 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org Subject: ports/20219: New port: biology/sim4 Message-ID: <E13HoDQ-000IzF-00@fling.sanbi.ac.za>
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>Number: 20219 >Category: ports >Synopsis: New port: biology/sim4 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Thu Jul 27 07:10:00 PDT 2000 >Closed-Date: >Last-Modified: >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: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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