pkg/43777: Update biology/lucy to 1.20

[kamelderouiche%yahoo.com@localhost]

>Number:         43777
>Category:       pkg
>Synopsis:       Update biology/lucy to 1.20
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    pkg-manager
>State:          open
>Class:          sw-bug
>Submitter-Id:   net
>Arrival-Date:   Wed Aug 18 11:05:00 +0000 2010
>Originator:     Derouiche
>Release:        NetBSD 5.0.2
>Organization:
>Environment:
NetBSD ToraboraServer 5.0.2 NetBSD 5.0.2 (GENERIC) #0: Sat Feb  6 17:53:27 UTC 
2010  
builds%b7.netbsd.org@localhost:/home/builds/ab/netbsd-5-0-2-RELEASE/i386/201002061851Z-obj/home/builds/ab/netbsd-5-0-2-RELEASE/src/sys/arch/i386/compile/GENERIC
 i386

>Description:
amont-changes:
=============
Version 1.20, 9/3/2008.  This version fixes a bug that caused lucy
to fail when there was too much information on the FASTA header lines
in the input files.  Lucy had a 256 character buffer for reading
lines from the input files.  If any FASTA header lines were longer
than 256 characters, the remaining characters would get read as part
of the FASTA sequence.  The solution implemented in this version is
simply to increase the buffer size to 4096 characters.  While that
still leaves the potential for the same error to occur with extremely
long header lines, the limitation that this entails seems reasonable,
and this should fix the problem for all pratical purposes.

---------------------------------------------------------------------
Version 1.19, 12/30/2003.  This version fixes a bug that could cause
sequences to be rejected incorrectly in the vector detection step
(phase 6).  Because of the way that lucy compares "tags" in the
target sequence with "tags" in the vector sequence, some bases in
the target sequence could get counted more than once in the tally
of bases that match the vector sequence.  In rare instances, this
could cause the sequence to exceed the minimum threshold for
rejection, as a result of random sequence similarity.

The reporting of the CLB range in the -debug output file has also
been changed.  If the CLB range begins with the first base of the
sequence, then the left coordinate of the CLB range will be reported
as 1 (instead of 0).  The range "CLB 0 0" still indicates an empty
CLB range.

---------------------------------------------------------------------
Version 1.18, 2/20/2003.  This version fixes a bug that could cause
lucy to crash.  If the size of the largest sequence in the batch to 
be processed was less than the sum of the alignment ranges (200 by 
default), earlier versions of lucy could crash.  The alignment ranges 
are controlled by the -range parameter.

>How-To-Repeat:
n/a
>Fix:
$diff -ruN Makefile.orig Makefile
--- Makefile.orig       2010-08-18 11:05:09.000000000 +0000
+++ Makefile    2010-08-18 11:30:32.000000000 +0000
@@ -1,22 +1,25 @@
-# $NetBSD: Makefile,v 1.5 2009/05/16 23:40:13 zafer Exp $
+# $NetBSD$
 #
 
-DISTNAME=              lucy-1.18p
-CATEGORIES=            biology
-MASTER_SITES=          # ftp://ftp.tigr.org/pub/software/Lucy/
-
-MAINTAINER=            dprice%cs.nmsu.edu@localhost
-HOMEPAGE=              http://lucy.sourceforge.net/
-COMMENT=               Sequence Cleanup Program
+DISTNAME=      lucy1.20
+PKGNAME=       lucy-1.20
+CATEGORIES=    biology
+MASTER_SITES=  http://garr.dl.sourceforge.net/project/lucy/lucy/lucy%201.20/
+
+MAINTAINER=    dprice%cs.nmsu.edu@localhost
+HOMEPAGE=      http://lucy.sourceforge.net/
+COMMENT=       Sequence Cleanup Program
 
 PKG_INSTALLATION_TYPES=        overwrite pkgviews
 PKG_DESTDIR_SUPPORT=   user-destdir
 
-AUTO_MKDIRS=           yes
+WRKSRC=        ${WRKDIR}/lucy-1.20p
+
+INSTALLATION_DIRS+=    bin ${PKGMANDIR}/man1 share/examples/lucy
 
 do-install:
-       ${INSTALL_PROGRAM} ${WRKSRC}/lucy ${DESTDIR}${PREFIX}/bin
-       ${INSTALL_DATA} ${WRKSRC}/lucy.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
+       ${INSTALL_PROGRAM} ${WRKSRC}/lucy ${DESTDIR}${PREFIX}/bin/
+       ${INSTALL_MAN} ${WRKSRC}/lucy.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
        cd ${WRKSRC} && ${INSTALL_DATA} PUC19 PUC19splice PUC19splice.for \
                PUC19splice.rev atie.seq atie.qul atie.2nd pSPORT1splice \
                pSPORT1vector ARMTM40TR.seq ARMTM40TR.qul lucy.ps lucy.debug \

$diff -ruN PLIST.orig PLIST
--- PLIST.orig  2010-08-18 11:05:09.000000000 +0000
+++ PLIST       2010-08-18 11:31:45.000000000 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2009/06/12 19:07:29 rillig Exp $
+@comment $NetBSD$
 bin/lucy
 man/man1/lucy.1
 share/examples/lucy/ARMTM40TR.qul