Add p5-AcePerl, a perl interface to the ACEDB genome database system

PR:		ports/20223
Submitted by:	Johann Visagie <johann@egenetics.com>

9 files changed, 177 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index d91b479913aa..e0504574c68f 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -11,6 +11,7 @@
     SUBDIR += molden
     SUBDIR += mopac
     SUBDIR += ortep3
+    SUBDIR += p5-AcePerl
     SUBDIR += paml
     SUBDIR += phylip
     SUBDIR += platon
diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile
new file mode 100644
index 000000000000..11e90f57696a
--- /dev/null
+++ b/biology/p5-AcePerl/Makefile
@@ -0,0 +1,37 @@
+# New ports collection makefile for:	p5-AcePerl
+# Date created:		26 July 2000
+# Whom:	      		Johann Visagie <johann@egenetics.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	AcePerl
+PORTVERSION=	1.62
+CATEGORIES=	biology databases perl5
+MASTER_SITES=	http://stein.cshl.org/AcePerl/archive/ \
+		${MASTER_SITE_PERL_CPAN}
+MASTER_SITE_SUBDIR=Ace
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	johann@egenetics.com
+
+USE_PERL5=	YES
+
+MAN3=		Ace::Sequence::Feature.3 \
+		Ace::Sequence.3 \
+		Ace.3 \
+		Ace::Sequence::FeatureList.3 \
+		Ace::Sequence::Multi.3 \
+		Ace::Sequence::Homol.3 \
+		Ace::Object.3 \
+		Ace::Local.3 \
+		Ace::Iterator.3 \
+		Ace::Model.3
+
+MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
+
+do-configure:
+	${CP} ${FILESDIR}/FREEBSD_DEF ${WRKSRC}/ace/wmake/
+	@ cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL
+
+.include <bsd.port.mk>
diff --git a/biology/p5-AcePerl/distinfo b/biology/p5-AcePerl/distinfo
new file mode 100644
index 000000000000..9f0e26a085ea
--- /dev/null
+++ b/biology/p5-AcePerl/distinfo
@@ -0,0 +1 @@
+MD5 (AcePerl-1.62.tar.gz) = d9978077a8e1857b94216d5a28bc38ef
diff --git a/biology/p5-AcePerl/files/FREEBSD_DEF b/biology/p5-AcePerl/files/FREEBSD_DEF
new file mode 100644
index 000000000000..685175adcd87
--- /dev/null
+++ b/biology/p5-AcePerl/files/FREEBSD_DEF
@@ -0,0 +1,23 @@
+#################################################################
+############### acedb: R.Durbin and J.Thierry-Mieg ##############
+#################################################################
+
+#################################################################
+########### This file is included by wmake/truemake #############
+######  Edit this file to adapt the ACeDB to a new machine ######
+#####   following the explanations given in wmake/truemake  #####
+#################################################################
+
+CFLAGS+= -g -Wall -O2 -DACEDB4
+NAME = FREEBSD
+COMPILER = gcc ${CFLAGS}
+LINKER = gcc -g
+
+LIBS = -lm
+Xt_LIBS = -L/usr/X11R6/lib -lXaw -lXt -lXmu -lXext -lX11
+LEX_LIBS = 
+
+RPCGEN_FLAGS = -b -I -K -1
+
+#################################################################
+#################################################################
diff --git a/biology/p5-AcePerl/files/patch-aa b/biology/p5-AcePerl/files/patch-aa
new file mode 100644
index 000000000000..add3f24ba66b
--- /dev/null
+++ b/biology/p5-AcePerl/files/patch-aa
@@ -0,0 +1,22 @@
+--- ace/wh/mystdlib.h.orig	Fri Jul  2 23:04:55 1999
++++ ace/wh/mystdlib.h	Thu Jul 27 17:20:19 2000
+@@ -161,7 +161,7 @@
+ #endif
+ 
+ #if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \
+-	defined(HP) || defined(WIN32)
++	defined(HP) || defined(WIN32) || defined(FREEBSD)
+ 
+ #ifdef WIN32
+ #include <mbctype.h>
+--- ace/wh/mydirent.h.orig	Mon Jan 11 01:51:40 1999
++++ ace/wh/mydirent.h	Thu Jul 27 17:20:41 2000
+@@ -55,7 +55,7 @@
+ extern char *getwd(char *pathname) ;
+ #endif /* HP || SOLARIS || WIN32 */
+ 
+-#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP)
++#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined(FREEBSD)
+ #include <dirent.h>
+   typedef struct dirent MYDIRENT ;
+ #endif
diff --git a/biology/p5-AcePerl/files/patch-ab b/biology/p5-AcePerl/files/patch-ab
new file mode 100644
index 000000000000..2ad84954665b
--- /dev/null
+++ b/biology/p5-AcePerl/files/patch-ab
@@ -0,0 +1,11 @@
+--- ace/memsubs.c.orig	Mon Jan 11 02:01:29 1999
++++ ace/memsubs.c	Thu Jul 27 17:18:45 2000
+@@ -21,7 +21,7 @@
+ #if defined(NEXT) || defined(HP) || defined(MACINTOSH) 
+ extern void* malloc(mysize_t size) ;
+ #elif !defined(WIN32)
+-#include <malloc.h>   /* normal machines  */
++#include <stdlib.h>   /* normal machines  */
+ #endif
+ 
+ /********** primary type definition **************/
diff --git a/biology/p5-AcePerl/pkg-comment b/biology/p5-AcePerl/pkg-comment
new file mode 100644
index 000000000000..ff9627c37254
--- /dev/null
+++ b/biology/p5-AcePerl/pkg-comment
@@ -0,0 +1 @@
+Perl interface to the ACEDB genome database system
diff --git a/biology/p5-AcePerl/pkg-descr b/biology/p5-AcePerl/pkg-descr
new file mode 100644
index 000000000000..b282dac21cd5
--- /dev/null
+++ b/biology/p5-AcePerl/pkg-descr
@@ -0,0 +1,8 @@
+AcePerl is an object-oriented Perl interface for the ACEDB genome database
+system. It provides functionality for connecting to remote ACEDB databases,
+performing queries, fetching ACE objects, and updating databases.
+
+WWW: http://stein.cshl.org/AcePerl/
+
+- Johann
+johann@egenetics.com
diff --git a/biology/p5-AcePerl/pkg-plist b/biology/p5-AcePerl/pkg-plist
new file mode 100644
index 000000000000..0de06a9b8076
--- /dev/null
+++ b/biology/p5-AcePerl/pkg-plist
@@ -0,0 +1,73 @@
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.bs
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.so
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Local.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Model.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Object.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Iterator.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF/Filehandle.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/auto_save.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/date_style.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_to_ace_date.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_row.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_tree.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asAce.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isTimestamp.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asGif.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asHTML.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/autosplit.ix
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/commit.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/status.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_file.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/class_count.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/layout.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/pick.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/autosplit.ix
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/grep.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/put.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/new.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/classes.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_register_iterator.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/find.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/ping.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/count.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/timestamps.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/.packlist
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace