From owner-freebsd-ports Tue Dec 18 18:31: 8 2001 Delivered-To: freebsd-ports@hub.freebsd.org Received: from freefall.freebsd.org (freefall.FreeBSD.org [216.136.204.21]) by hub.freebsd.org (Postfix) with ESMTP id E49CA37B41E for ; Tue, 18 Dec 2001 18:30:04 -0800 (PST) Received: (from gnats@localhost) by freefall.freebsd.org (8.11.6/8.11.6) id fBJ2U4f24192; Tue, 18 Dec 2001 18:30:04 -0800 (PST) (envelope-from gnats) Received: from c31516.thorn1.nsw.optusnet.com.au (yellow.biolateral.com.au [129.78.217.60]) by hub.freebsd.org (Postfix) with ESMTP id 80A6E37B405 for ; Tue, 18 Dec 2001 18:27:30 -0800 (PST) Received: (from tonym@localhost) by c31516.thorn1.nsw.optusnet.com.au (8.11.6/8.11.6) id fBJ2RSL46039; Wed, 19 Dec 2001 13:27:28 +1100 (EST) (envelope-from tonym) Message-Id: <200112190227.fBJ2RSL46039@c31516.thorn1.nsw.optusnet.com.au> Date: Wed, 19 Dec 2001 13:27:28 +1100 (EST) From: Tony Maher Reply-To: Tony Maher To: FreeBSD-gnats-submit@freebsd.org X-Send-Pr-Version: 3.113 Subject: ports/32998: New port: biology/dna-qc Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk List-ID: List-Archive: (Web Archive) List-Help: (List Instructions) List-Subscribe: List-Unsubscribe: X-Loop: FreeBSD.org >Number: 32998 >Category: ports >Synopsis: New port: biology/dna-qc >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: Tue Dec 18 18:30:04 PST 2001 >Closed-Date: >Last-Modified: >Originator: Tony Maher >Release: FreeBSD 4.4-STABLE i386 >Organization: BioLateral >Environment: System: FreeBSD dt.home 4.4-STABLE FreeBSD 4.4-STABLE #1: Sun Dec 16 16:39:43 EST 2001 root@dt.home:/usr/obj/usr/src/sys/DT i386 >Description: White, O., T. Dunning, G. Sutton, M. Adams, J. C. Venter, and C. Fields (1993). A quality control algorithm for DNA sequencing projects. Nucleic Acids Research (in press)." - from the README file TIGR claim no copyright on this but it is derived from other software * "Copyright 1993, New Mexico State University * * All rights reserved, unlimited redistribution and modification * * allowed, except that this notice must be preserved and original * * authorship must be acknowledged. No warranty of fitness of * * purpose or merchantibility is express or implied, this software * * is available on an 'as is' basis." * * * *This header must be included in any distribution of this program or* *derivatives of this program. >How-To-Repeat: >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: # # dna-qc # dna-qc/files # dna-qc/files/patch-hybridize # dna-qc/files/patch-Makefile # dna-qc/files/patch-normalize # dna-qc/files/patch-random_line # dna-qc/files/patch-stringpool # dna-qc/pkg-plist # dna-qc/pkg-descr # dna-qc/pkg-comment # dna-qc/distinfo # dna-qc/Makefile # echo c - dna-qc mkdir -p dna-qc > /dev/null 2>&1 echo c - dna-qc/files mkdir -p dna-qc/files > /dev/null 2>&1 echo x - dna-qc/files/patch-hybridize sed 's/^X//' >dna-qc/files/patch-hybridize << 'END-of-dna-qc/files/patch-hybridize' X--- hybridize.c.orig Sat Nov 24 21:25:04 2001 X+++ hybridize.c Sat Nov 24 21:25:35 2001 X@@ -54,6 +54,7 @@ X extern unsigned array_to_base_4(); X extern unsigned string_to_base_4(); X extern int dna2i(); X+double logl(); X int *read_file(); X X main(argc, argv) END-of-dna-qc/files/patch-hybridize echo x - dna-qc/files/patch-Makefile sed 's/^X//' >dna-qc/files/patch-Makefile << 'END-of-dna-qc/files/patch-Makefile' X--- Makefile.orig Sat Nov 24 21:39:24 2001 X+++ Makefile Sat Nov 24 21:39:38 2001 X@@ -1,5 +1,5 @@ X #CC=cc X-CFLAGS += -g X+#CFLAGS += -g X LEX=flex X X END-of-dna-qc/files/patch-Makefile echo x - dna-qc/files/patch-normalize sed 's/^X//' >dna-qc/files/patch-normalize << 'END-of-dna-qc/files/patch-normalize' X--- normalize.c.orig Sat Nov 24 21:34:50 2001 X+++ normalize.c Sat Nov 24 21:35:09 2001 X@@ -6,7 +6,7 @@ X X #include X #include X-#include X+#include X X #define ELEMENT double X END-of-dna-qc/files/patch-normalize echo x - dna-qc/files/patch-random_line sed 's/^X//' >dna-qc/files/patch-random_line << 'END-of-dna-qc/files/patch-random_line' X--- random_line.c.orig Sat Nov 24 21:26:57 2001 X+++ random_line.c Sat Nov 24 21:31:24 2001 X@@ -63,7 +63,7 @@ X extern int optind; X X char *inname; X- char *fname[256]; X+ char fname[256]; X int ch, error_flag; X double divisor; X FILE *f_in, *f_out1, *f_out2; END-of-dna-qc/files/patch-random_line echo x - dna-qc/files/patch-stringpool sed 's/^X//' >dna-qc/files/patch-stringpool << 'END-of-dna-qc/files/patch-stringpool' X--- stringpool.c.orig Sat Nov 24 21:32:12 2001 X+++ stringpool.c Sat Nov 24 21:34:26 2001 X@@ -61,7 +61,7 @@ X static int current_generation=0; X static char *pool=NULL; X X-static void allocate_pool() X+void allocate_pool() X { X if (pool_size > 0) { /* a growing pool handles enormous words */ X pool_size = 2*pool_size; /* but grows less and less often */ END-of-dna-qc/files/patch-stringpool echo x - dna-qc/pkg-plist sed 's/^X//' >dna-qc/pkg-plist << 'END-of-dna-qc/pkg-plist' Xbin/counter Xbin/hybridize Xbin/normalize Xbin/random_clip Xbin/random_line X%%PORTDOCS%%share/doc/dna-qc/qc_algorithm.ps.Z X%%PORTDOCS%%share/doc/dna-qc/qc_fig1.ps.Z X%%PORTDOCS%%share/doc/dna-qc/qc_fig2a.ps.Z X%%PORTDOCS%%share/doc/dna-qc/qc_fig2b.ps.Z X%%PORTDOCS%%share/doc/dna-qc/qc_fig2c.ps.Z X%%PORTDOCS%%share/doc/dna-qc/qc_fig3.ps.Z X%%PORTDOCS%%share/doc/dna-qc/qc_fig4.ps.Z X%%PORTDOCS%%share/doc/dna-qc/qc_fig5.ps.Z X%%PORTDOCS%%share/doc/dna-qc/qc_fig6.ps.Z X%%PORTDOCS%%share/doc/dna-qc/qc_fig7.ps.Z X%%PORTDOCS%%share/doc/dna-qc/surprize.ps.Z X%%PORTDOCS%%share/examples/dna-qc/README X%%PORTDOCS%%share/examples/dna-qc/script.compare X%%PORTDOCS%%share/examples/dna-qc/script.limits X%%PORTDOCS%%share/examples/dna-qc/bact.all X%%PORTDOCS%%share/examples/dna-qc/chromosomeIII.all X%%PORTDOCS%%share/examples/dna-qc/human.all X%%PORTDOCS%%share/examples/dna-qc/worm.all X%%PORTDOCS%%@dirrm share/doc/dna-qc X%%PORTDOCS%%@dirrm share/examples/dna-qc END-of-dna-qc/pkg-plist echo x - dna-qc/pkg-descr sed 's/^X//' >dna-qc/pkg-descr << 'END-of-dna-qc/pkg-descr' X"relevant reference: XWhite, O., T. Dunning, G. Sutton, M. Adams, J. C. Venter, and C. XFields (1993). A quality control algorithm for DNA sequencing Xprojects. Nucleic Acids Research (in press)." X- from the README file X X-- XTony Maher END-of-dna-qc/pkg-descr echo x - dna-qc/pkg-comment sed 's/^X//' >dna-qc/pkg-comment << 'END-of-dna-qc/pkg-comment' XA quality control algorithm for DNA sequencing projects END-of-dna-qc/pkg-comment echo x - dna-qc/distinfo sed 's/^X//' >dna-qc/distinfo << 'END-of-dna-qc/distinfo' XMD5 (qc.tar.Z) = 30dc287fa9c7c8e818d4ce0a34b86422 XMD5 (hyb2dis.txt) = e5b8260c84a822cb0deff264f01331b8 END-of-dna-qc/distinfo echo x - dna-qc/Makefile sed 's/^X//' >dna-qc/Makefile << 'END-of-dna-qc/Makefile' X# New ports collection makefile for: dna-qc X# Date created: 25 Novemeber 2001 X# Whom: Tony Maher X# X# $FreeBSD$ X# X XPORTNAME= dna-qc XPORTVERSION= 1993.07.26 XCATEGORIES= biology XMASTER_SITES= ftp://ftp.tigr.org/pub/software/qc/ XDISTNAME= qc XEXTRACT_SUFX= .tar.Z X XMAINTAINER= tonym@biolateral.com.au X XNO_WRKSUBDIR= true X XEXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME} XEXAMPLES= README script.compare script.limits \ X bact.all chromosomeIII.all human.all worm.all XPROGRAMS= counter hybridize normalize random_clip random_line X Xdo-install: X cd ${WRKSRC}; \ X for file in ${PROGRAMS}; do \ X ${INSTALL_PROGRAM} $$file ${PREFIX}/bin; \ X done X Xpost-install: X for file in ${PROGRAMS}; do \ X strip ${PREFIX}/bin/$$file; \ X done X.if !defined(NOPORTDOCS) X ${MKDIR} ${DOCSDIR} X ${MKDIR} ${EXAMPLESDIR} X cd ${WRKDIR}; \ X for file in ${EXAMPLES}; do \ X ${INSTALL_DATA} $$file ${EXAMPLESDIR}; \ X done X cd ${WRKDIR}/qc_doc; \ X for file in *; do \ X ${INSTALL_DATA} $$file ${DOCSDIR}; \ X done X cd ${WRKDIR}/surprize_doc; \ X for file in *; do \ X ${INSTALL_DATA} $$file ${DOCSDIR}; \ X done X.endif X X.include END-of-dna-qc/Makefile exit >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message