Date: Wed, 19 Dec 2001 13:27:28 +1100 (EST) From: Tony Maher <tonym@biolateral.com.au> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/32998: New port: biology/dna-qc Message-ID: <200112190227.fBJ2RSL46039@c31516.thorn1.nsw.optusnet.com.au>
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>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 <stdio.h>
X #include <math.h>
X-#include <malloc.h>
X+#include <stdlib.h>
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 <tonym@biolateral.com.au>
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 <bsd.port.mk>
END-of-dna-qc/Makefile
exit
>Release-Note:
>Audit-Trail:
>Unformatted:
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