30 files changed, 0 insertions, 726 deletions

diff --git a/biology/L-Breeder/Makefile b/biology/L-Breeder/Makefile
deleted file mode 100644
index 6bbd2a53b371..000000000000
--- a/biology/L-Breeder/Makefile
+++ /dev/null
@@ -1,50 +0,0 @@
-# ex:ts=8
-# New ports collection makefile for:	L-Breeder
-# Date created:				30 May 2002
-# Whom:					David Yeske <dyeske@gmail.com> et al
-#
-# $FreeBSD$
-#
-
-PORTNAME=	LBreeder
-PORTVERSION=	1.0
-PORTREVISION=	15
-CATEGORIES=	biology
-MASTER_SITES=	http://www.simonyi.ox.ac.uk/dawkins/software/yan/L-Breeder/
-DISTNAME=	${PORTNAME}-source
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Allows you to display and breed L-system forms
-
-DEPRECATED=	Looks like an abandonware, no more public distfile
-EXPIRATION_DATE=	2011-08-01
-
-NO_WRKSUBDIR=	yes
-BUILD_WRKSRC=	${WRKSRC}/Unix
-
-USE_ZIP=	yes
-USE_GL=		glut
-USE_GMAKE=	yes
-USE_WX=		2.4
-
-.if defined(WITH_OPTIMIZED_CFLAGS)
-CFLAGS+=	-O3 -ffast-math
-.endif
-
-pre-everything::
-.if !defined(WITH_OPTIMIZED_CFLAGS)
-	@${ECHO_MSG} "You can enable additional compilation optimizations"
-	@${ECHO_MSG} "by defining WITH_OPTIMIZED_CFLAGS"
-.endif
-
- 
-do-install:
-	@${INSTALL_PROGRAM} ${BUILD_WRKSRC}/${PORTNAME} ${PREFIX}/bin
-.if !defined(NOPORTDOCS)
-	@${MKDIR} ${DOCSDIR}
-	@${INSTALL_DATA} ${WRKSRC}/documentation/* ${DOCSDIR}
-.endif
-	@${MKDIR} ${EXAMPLESDIR}
-	@${INSTALL_DATA} ${WRKSRC}/Lsystems/* ${EXAMPLESDIR}
-
-.include <bsd.port.mk>
diff --git a/biology/L-Breeder/distinfo b/biology/L-Breeder/distinfo
deleted file mode 100644
index 2eb9ac2f0c64..000000000000
--- a/biology/L-Breeder/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (LBreeder-source.zip) = e6c5189a3b3bfdc6911a1cd0cba3f440f2e4fa67d9cadc411ded1f6b1400026a
-SIZE (LBreeder-source.zip) = 131306
diff --git a/biology/L-Breeder/files/patch-Unix-Makefile b/biology/L-Breeder/files/patch-Unix-Makefile
deleted file mode 100644
index 2c598185d3dd..000000000000
--- a/biology/L-Breeder/files/patch-Unix-Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
---- Unix/Makefile.orig	Fri Jul  2 10:06:30 2004
-+++ Unix/Makefile	Wed Dec  7 07:46:56 2005
-@@ -1,9 +1,10 @@
- src=../src/
-+C_FLAGS= -I$(LOCALBASE)/include
- 
- .PHONY : clean all
- 
- all          : probability.o mutprobs.o trackball.o Lparse.o GL_Ldraw.o Lline.o Lsys.o GLUT_LBreeder.o
--	g++ probability.o mutprobs.o trackball.o Lparse.o GL_Ldraw.o Lline.o Lsys.o GLUT_LBreeder.o ${src}main.cpp -lGL -lGLU -lglut -o LBreeder-${OSTYPE}
-+	g++ probability.o mutprobs.o trackball.o Lparse.o GL_Ldraw.o Lline.o Lsys.o GLUT_LBreeder.o ${src}main.cpp -L$(LOCALBASE)/lib -lGL -lGLU -lglut -o LBreeder
- 
- GLUT_LBreeder.o : ${src}GLUT_LBreeder.cpp  ${src}GLUT_LBreeder.h
- 	g++ -c  ${src}GLUT_LBreeder.cpp ${C_FLAGS}
diff --git a/biology/L-Breeder/pkg-descr b/biology/L-Breeder/pkg-descr
deleted file mode 100644
index 43d1ced471b4..000000000000
--- a/biology/L-Breeder/pkg-descr
+++ /dev/null
@@ -1,4 +0,0 @@
-L-Breeder is a program which allows you to display, breed, and
-genetically engineered L-system forms.
-
-WWW: http://www.simonyi.ox.ac.uk/dawkins/software/yan/L-Breeder/
diff --git a/biology/L-Breeder/pkg-plist b/biology/L-Breeder/pkg-plist
deleted file mode 100644
index 639fb1333198..000000000000
--- a/biology/L-Breeder/pkg-plist
+++ /dev/null
@@ -1,24 +0,0 @@
-bin/LBreeder
-%%PORTDOCS%%%%DOCSDIR%%/ReadMe.txt
-%%PORTDOCS%%%%DOCSDIR%%/commands.html
-%%PORTDOCS%%%%DOCSDIR%%/tutorial.html
-%%EXAMPLESDIR%%/AIRHORSE.LS
-%%EXAMPLESDIR%%/AXIS.LS
-%%EXAMPLESDIR%%/BASETREE.LS
-%%EXAMPLESDIR%%/FERN.LS
-%%EXAMPLESDIR%%/FRACT00.LS
-%%EXAMPLESDIR%%/FRACT01.LS
-%%EXAMPLESDIR%%/FRACT02.LS
-%%EXAMPLESDIR%%/FRACT03.LS
-%%EXAMPLESDIR%%/TREE00B.LS
-%%EXAMPLESDIR%%/TREE00C.LS
-%%EXAMPLESDIR%%/TREE02.LS
-%%EXAMPLESDIR%%/TREE03.LS
-%%EXAMPLESDIR%%/TREE04.LS
-%%EXAMPLESDIR%%/TREE05.LS
-%%EXAMPLESDIR%%/TREE06.LS
-%%EXAMPLESDIR%%/TREE07.LS
-%%EXAMPLESDIR%%/TREE11.LS
-%%EXAMPLESDIR%%/TROPISM.LS
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%EXAMPLESDIR%%
diff --git a/biology/Makefile b/biology/Makefile
index 90c4e325f7d0..5df882f719d5 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -3,7 +3,6 @@
 
     COMMENT = Biology
 
-    SUBDIR += L-Breeder
     SUBDIR += adun
     SUBDIR += ariadne
     SUBDIR += artemis
@@ -18,9 +17,7 @@
     SUBDIR += chemeq
     SUBDIR += clustalw
     SUBDIR += consed
-    SUBDIR += crimap
     SUBDIR += crux
-    SUBDIR += distribfold
     SUBDIR += dna-qc
     SUBDIR += dotter
     SUBDIR += embassy
@@ -39,13 +36,11 @@
     SUBDIR += hmmer
     SUBDIR += iolib
     SUBDIR += jalview
-    SUBDIR += kinemage
     SUBDIR += lagan
     SUBDIR += lamarc
     SUBDIR += libgenome
     SUBDIR += libsbml
     SUBDIR += linux-foldingathome
-    SUBDIR += lsysexp
     SUBDIR += mafft
     SUBDIR += mapm3
     SUBDIR += migrate
diff --git a/biology/crimap/Makefile b/biology/crimap/Makefile
deleted file mode 100644
index 80a641052dc4..000000000000
--- a/biology/crimap/Makefile
+++ /dev/null
@@ -1,51 +0,0 @@
-# New ports collection makefile for:	crimap
-# Date created:				4 December 2001
-# Whom:					Tony Maher <tonym@biolateral.com.au>
-#
-# $FreeBSD$
-#
-
-PORTNAME=	crimap
-PORTVERSION=	2.4
-PORTREVISION=	1
-CATEGORIES=	biology
-MASTER_SITES=	http://compgen.rutgers.edu/multimap/crimap/
-DISTNAME=	${PORTNAME}.source
-EXTRACT_SUFX=	.tar.Z
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Creation of multilocus linkage maps
-
-DEPRECATED=	Looks like an abandonware, no more public distfile
-EXPIRATION_DATE=	2011-08-01
-
-NO_WRKSUBDIR=	true
-
-PROGRAMS=	crimap
-EXAMPLES=	chr7a.gen demo.dat
-EXIT_PATCH=	e_ped.c get_log.c our_allo.c our_orde.c
-
-post-patch:
-.for file in ${EXIT_PATCH}
-	@${REINPLACE_CMD} -e 's|exit\ *()|exit(0)|' ${WRKSRC}/${file}
-.endfor
-
-do-build:
-	cd ${WRKSRC}; \
-	${CC} ${CFLAGS} -o crimap *.c -lm
-
-do-install:
-.for file in ${PROGRAMS}
-	${INSTALL_PROGRAM} ${WRKSRC}/${file} ${PREFIX}/bin
-.endfor
-.if !defined(NOPORTDOCS)
-	@${MKDIR} ${EXAMPLESDIR}
-	@${MKDIR} ${DOCSDIR}
-	${CAT} ${WRKSRC}/progdoc_v2.4 | tbl | eqn -Tlatin1 | nroff -ms -t \
-		> ${DOCSDIR}/progdoc_v2.4
-.for file in ${EXAMPLES}
-	${INSTALL_DATA} ${WRKSRC}/${file} ${EXAMPLESDIR}
-.endfor
-.endif
-
-.include <bsd.port.mk>
diff --git a/biology/crimap/distinfo b/biology/crimap/distinfo
deleted file mode 100644
index 7699f9fffbd5..000000000000
--- a/biology/crimap/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (crimap.source.tar.Z) = d45b372ad1427b32d0b607ee8cc5a9ba0afd5f48171926c559278338a93cf847
-SIZE (crimap.source.tar.Z) = 110217
diff --git a/biology/crimap/files/patch-defs.h b/biology/crimap/files/patch-defs.h
deleted file mode 100644
index 54e23c3a4ddd..000000000000
--- a/biology/crimap/files/patch-defs.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- ./defs.h.orig	1990-10-10 17:07:22.000000000 -0400
-+++ ./defs.h	2010-01-16 12:51:21.484797488 -0500
-@@ -17,7 +17,7 @@
- typedef short SHORT;
- typedef long ID;
- typedef long LINDEX;
--typedef int INT;
-+typedef long INT;
- 
- struct loci_orders{
-      SHORT num_loci;
diff --git a/biology/crimap/files/patch-our_allo.c b/biology/crimap/files/patch-our_allo.c
deleted file mode 100644
index 7062747d642d..000000000000
--- a/biology/crimap/files/patch-our_allo.c
+++ /dev/null
@@ -1,24 +0,0 @@
---- ./our_allo.c.orig	1989-04-04 12:36:21.000000000 -0400
-+++ ./our_allo.c	2010-01-16 12:50:32.073330216 -0500
-@@ -21,10 +21,11 @@
- static HEADER base;
- static HEADER *allocp = NULL;	
- 
-+static HEADER *morecore();
-+
- char *our_alloc(nbytes)
-         ALLOC nbytes;
- {
--	HEADER *morecore();
- 	HEADER *p;
- 	HEADER *q;
- 	ALLOC nunits;
-@@ -76,7 +77,7 @@
- 	cp = malloc(rnu * sizeof(HEADER));
- 	if (!cp) {
-            printf("\n ERROR: ALLOCATION FAILED IN MORECORE\n");
--           exit();  
-+           exit(0);  
-         }
- 	up = (HEADER *)cp;
- 	up->s.size = rnu;
diff --git a/biology/crimap/files/patch-our_orde.c b/biology/crimap/files/patch-our_orde.c
deleted file mode 100644
index 5479206d547c..000000000000
--- a/biology/crimap/files/patch-our_orde.c
+++ /dev/null
@@ -1,24 +0,0 @@
---- ./our_orde.c.orig	1989-04-04 12:36:22.000000000 -0400
-+++ ./our_orde.c	2010-01-16 12:50:32.076328932 -0500
-@@ -21,10 +21,11 @@
- static HEADER orders_base;
- static HEADER *orders_allocp = NULL;	
- 
-+static HEADER *orders_morecore();
-+
- char *our_orders_alloc(nbytes)
-         ALLOC nbytes;
- {
--	HEADER *orders_morecore();
- 	HEADER *p, *q;
- 	ALLOC nunits;
- 
-@@ -76,7 +77,7 @@
- 	cp = malloc(rnu * sizeof(HEADER));
- 	if (!cp) {
-          printf("\nALLOC FAILED IN OUR_ORDERS_ALLOC\n");
--         exit ();
-+         exit(0);
-         }
- 	up = (HEADER *)cp;
- 	up->s.size = rnu;
diff --git a/biology/crimap/pkg-descr b/biology/crimap/pkg-descr
deleted file mode 100644
index 7c3016894c1f..000000000000
--- a/biology/crimap/pkg-descr
+++ /dev/null
@@ -1,7 +0,0 @@
-"The main purpose of CRI-MAP is to allow rapid, largely automated
-construction of multilocus linkage maps (and facilitate the attendant
-tasks of assessing support relative to alternative locus orders,
-generating LOD tables, and detecting data errors)."
-- from the documentation
-
-WWW: http://compgen.rutgers.edu/multimap/crimap/
diff --git a/biology/crimap/pkg-plist b/biology/crimap/pkg-plist
deleted file mode 100644
index c58d2e87d84e..000000000000
--- a/biology/crimap/pkg-plist
+++ /dev/null
@@ -1,6 +0,0 @@
-bin/crimap
-%%PORTDOCS%%%%DOCSDIR%%/progdoc_v2.4
-%%PORTDOCS%%%%EXAMPLESDIR%%/chr7a.gen
-%%PORTDOCS%%%%EXAMPLESDIR%%/demo.dat
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
diff --git a/biology/distribfold/Makefile b/biology/distribfold/Makefile
deleted file mode 100644
index b0de90c56412..000000000000
--- a/biology/distribfold/Makefile
+++ /dev/null
@@ -1,133 +0,0 @@
-# New ports collection makefile for:	folding@home client
-# Date created:		Sun Sep 29 19:48:01 UTC 2002
-# Whom:			Mario Sergio Fujikawa Ferreira <lioux@FreeBSD.org>
-#
-# $FreeBSD$
-#
-
-PORTNAME=	distribfold
-PORTVERSION=	0.1.${RELEASE_DATE}
-CATEGORIES=	biology net
-MASTER_SITES=	${MASTER_SITE_LOCAL}
-MASTER_SITE_SUBDIR=	lioux
-DISTNAME=	distribfold-current-FreeBSD-${PORTVERSION}
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	distributedfolding.org distributed protein folding project
-
-LIB_DEPENDS=	c_r.4:${PORTSDIR}/misc/compat4x
-
-DEPRECATED=	No more upstream, looks like an abandonware
-EXPIRATION_DATE=	2011-08-01
-
-ONLY_FOR_ARCHS=	i386
-USE_BZIP2=	yes
-NO_BUILD=	yes
-
-WRKSRC=		${WRKDIR}/distribfold
-PKGMESSAGE=	${WRKDIR}/pkg-message
-SUB_FILES=	pkg-message
-
-# files to install
-SCRIPT_FILES=	distrib-update foldit
-PROGRAM_FILES=	foldtrajlite
-# installation dir
-DESTINATION_DIR=	${PREFIX}/distribfold
-
-# default users
-DNETFOLD_USER=dnetfold
-DNETFOLD_GROUP=dnetfold
-USERS=		${DNETFOLD_USER}
-GROUPS=		${DNETFOLD_GROUP}
-
-# default number of processors
-WITH_NCPU?=	1
-
-RELEASE_DATE=	20040613
-
-post-patch:
-	@${REINPLACE_CMD} -E -e 's|%%DESTINATION_DIR%%|${DESTINATION_DIR}/cpu0|' \
-		${WRKSRC}/foldit
-
-do-install:
-# remove any patch scrap files
-.for ext in bak orig
-	@${RM} -f ${WRKSRC}/*.${ext}
-.endfor
-# strip binaries
-.for f in ${PROGRAM_FILES}
-	@${STRIP_CMD} ${WRKSRC}/${f}
-.endfor
-# install startup script
-	@${INSTALL_SCRIPT} ${WRKDIR}/distribfold.sh ${PREFIX}/etc/rc.d
-# for every cpu directory
-	@ncpu=`${CAT} ${WRKDIR}/ncpu` ; \
-	for dir in `${SH} ${FILESDIR}/number_of_dirs.sh $${ncpu}` ; do \
-		DESTINATION_DIR=${DESTINATION_DIR}/cpu$${dir} ; \
-		${MKDIR} $${DESTINATION_DIR} ; \
-		${INSTALL_DATA} ${WRKSRC}/* $${DESTINATION_DIR} ; \
-		${CHGRP} -R ${DNETFOLD_GROUP} $${DESTINATION_DIR} ; \
-		${CHMOD} g+w $${DESTINATION_DIR} ; \
-		${CHOWN} ${DNETFOLD_USER} $${DESTINATION_DIR}/* ; \
-		${CHMOD} u+w $${DESTINATION_DIR}/* ; \
-		for f in ${PROGRAM_FILES} ${SCRIPT_FILES} ; do \
-			${CHMOD} 0755 $${DESTINATION_DIR}/$${f} ; \
-		done ; \
-	done
-# display package message
-	@${CAT} ${PKGMESSAGE}
-
-post-install: cook-install-plist fix-startup-scripts
-
-pre-everything::
-.if ${WITH_NCPU} < 1
-	@${ECHO_MSG} "===> Number of processors HAS to be at least 1"
-	@${ECHO_MSG} "===> (${WITH_NCPU}) IS NOT"
-	@${FALSE}
-.endif
-	@${ECHO_MSG} "=======> ATTENTION <======="
-	@${ECHO_MSG} "===> If you want to have multiple copies of this program"
-	@${ECHO_MSG} "===> running in order to make better use of your SMP"
-	@${ECHO_MSG} "===> system, set WITH_CPU to the number of cpus"
-	@${ECHO_MSG} "===> available in your system"
-	@${ECHO_MSG} "===> For example, 2 cpus. \"make WITH_CPU=2\""
-	@${ECHO_MSG} "===> Do not use this variable if you do not have a SMP"
-	@${ECHO_MSG} "===> system. There is no advantage otherwise."
-
-do-configure:
-# prepare startup script
-	@${SED} -e 's|%%DNETFOLD_USER%%|${DNETFOLD_USER}|' \
-		-e 's|%%DESTINATION_DIR%%|${DESTINATION_DIR}|' \
-		-e 's|%%NCPU%%|${WITH_NCPU}|' \
-		${FILESDIR}/distribfold.sh > ${WRKDIR}/distribfold.sh
-# record number of cpus
-	@${ECHO} ${WITH_NCPU} > ${WRKDIR}/ncpu
-
-cook-install-plist: generate-plist
-.if ${WITH_NCPU} > 1
-	@${GREP} cpu0 ${TMPPLIST} > ${WRKDIR}/plist
-	@${TAIL} -n 2 ${TMPPLIST} > ${WRKDIR}/plist.end
-	@${CP} /dev/null ${WRKDIR}/plistN
-# for every cpu directory
-	@ncpu=`${CAT} ${WRKDIR}/ncpu` ; \
-	for dir in `${FILESDIR}/number_of_dirs.sh $${ncpu}` ; do \
-		${SED} -e "s|cpu0|cpu$${dir}|" ${WRKDIR}/plist >> ${WRKDIR}/plistN ; \
-	done
-	@${CP} /dev/null ${TMPPLIST}
-.for f in plistN plist.end
-	@${CAT} ${WRKDIR}/${f} >> ${TMPPLIST}
-.endfor
-.endif
-
-fix-startup-scripts:
-.if ${WITH_NCPU} > 1
-# for every cpu directory
-	@ncpu=`${CAT} ${WRKDIR}/ncpu` ; \
-	for dir in `${FILESDIR}/number_of_dirs.sh $${ncpu}` ; do \
-		${REINPLACE_CMD} -e "s|cpu0|cpu$${dir}|" \
-			${DESTINATION_DIR}/cpu$${dir}/foldit ; \
-		${RM} -f ${DESTINATION_DIR}/cpu$${dir}/foldit.bak ; \
-	done
-.endif
-
-.include <bsd.port.mk>
diff --git a/biology/distribfold/distinfo b/biology/distribfold/distinfo
deleted file mode 100644
index 6fc5bff43edc..000000000000
--- a/biology/distribfold/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (distribfold-current-FreeBSD-0.1.20040613.tar.bz2) = 92d2618710bd7840b949cfc38202235f7c19646e1820ab915b3ac9cbee690578
-SIZE (distribfold-current-FreeBSD-0.1.20040613.tar.bz2) = 9896091
diff --git a/biology/distribfold/files/distribfold.sh b/biology/distribfold/files/distribfold.sh
deleted file mode 100644
index 1ae040465297..000000000000
--- a/biology/distribfold/files/distribfold.sh
+++ /dev/null
@@ -1,61 +0,0 @@
-#!/bin/sh
-# taken from misc/dnetc by dbaker@distributed.net
-
-prefix="%%DESTINATION_DIR%%"
-ncpu=%%NCPU%%
-
-case "$1" in
-start)
-	while [ ${ncpu} -gt 0 ];
-	do
-		# update cpu count
-		ncpu=$((${ncpu} - 1))
-
-		# dir for current cpu
-		dir="${prefix}/cpu${ncpu}"
-
-		if [ ! -d $dir ]; then
-		 logger -i "distribfold client directory doesn't exist. ($dir)."
-		 exit
-		fi
-
-		if [ ! -f $dir/foldtrajlite ]; then
-		 logger -i "distribfold client doesn't exist. ($dir/dfoldtrajlite)."
-		 exit
-		fi
-
-		if [ ! -f $dir/handle.txt ]; then
-		 logger -i "distribfold client is not configured. 'su -m %%DNETFOLD_USER%% -c $dir/foldit' to configure it."
-		 echo "distribfold client is not configured. 'su -m %%DNETFOLD_USER%% -c $dir/foldit' to configure it."
-		 exit
-		fi
-
-		# start client for current cpu
-		su -m %%DNETFOLD_USER%% -c "cd $dir && ./foldit" 2>/dev/null >/dev/null &
-	done
-
-	echo -n " distribfold"
-	;;
-stop)
-	while [ ${ncpu} -gt 0 ];
-	do
-		# update cpu count
-		ncpu=$((${ncpu} - 1))
-
-		# dir for current cpu
-		dir="${prefix}/cpu${ncpu}"
-
-		rm -f $dir/foldtrajlite.lock
-	done
-
-	# give clients enough time to shutdown
-	# 5 seconds minimum + 5 seconds per number of clients
-	sleep $((5 + $((5 * ${ncpu})))) && echo -n " distribfold"
-	;;
-*)
-	echo "Usage: `basename $0` {start|stop}" >&2
-	exit 64
-	;;
-esac
-
-exit 0
diff --git a/biology/distribfold/files/number_of_dirs.sh b/biology/distribfold/files/number_of_dirs.sh
deleted file mode 100644
index bdb3b87cc56b..000000000000
--- a/biology/distribfold/files/number_of_dirs.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/sh
-
-ncpu=${1}
-current_list=""
-
-while [ ${ncpu} -gt 0 ];
-do
-	# update cpu count
-	ncpu=$((${ncpu} - 1))
-
-	current_list="${current_list} ${ncpu}"
-done
-
-echo ${current_list}
-
-exit 0
diff --git a/biology/distribfold/files/patch-foldit b/biology/distribfold/files/patch-foldit
deleted file mode 100644
index 3543505e05e8..000000000000
--- a/biology/distribfold/files/patch-foldit
+++ /dev/null
@@ -1,16 +0,0 @@
---- foldit.orig	Sun Sep 29 16:49:55 2002
-+++ foldit	Sun Sep 29 16:50:42 2002
-@@ -1,4 +1,7 @@
- #!/bin/sh
-+
-+cd %%DESTINATION_DIR%%
-+
- if [ -f donename.dat ]
- then
- 	rm -f tmpfoldit.bat
-@@ -23,4 +26,4 @@
- 		fi
- 	fi	
- fi	
--./foldtrajlite -f protein -n native 
-+exec ./foldtrajlite -f protein -n native 
diff --git a/biology/distribfold/files/pkg-message.in b/biology/distribfold/files/pkg-message.in
deleted file mode 100644
index 34551fa6fc6b..000000000000
--- a/biology/distribfold/files/pkg-message.in
+++ /dev/null
@@ -1,13 +0,0 @@
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-! REMEMBER REMEMBER REMEMBER REMEMBER REMEMBER REMEMBER REMEMBER REMEMBER !
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-You have to run '%%PREFIX%%/distribfold/cpu0/foldit' to configure it
-BEFORE trying to use distribfold.
-
-It will ask you questions on how it should work. It will NOT work
-if you do not run it and answer these questions.
-
-Do it now before you forget.
diff --git a/biology/distribfold/pkg-deinstall b/biology/distribfold/pkg-deinstall
deleted file mode 100644
index 82acb8daa0fc..000000000000
--- a/biology/distribfold/pkg-deinstall
+++ /dev/null
@@ -1,63 +0,0 @@
-#! /bin/sh
-#
-# $FreeBSD: /tmp/pcvs/ports/biology/distribfold/Attic/pkg-deinstall,v 1.1 2002-10-07 03:07:13 lioux Exp $
-# taken from net/cvsup-mirror
-
-PATH=/bin:/usr/sbin
-
-DNETFOLD_USER=${DNETFOLD_USER:-dnetfold}
-DNETFOLD_GROUP=${DNETFOLD_GROUP:-dnetfold}
-
-ask() {
-    local question default answer
-
-    question=$1
-    default=$2
-    if [ -z "${PACKAGE_BUILDING}" ]; then
-	read -p "${question} [${default}]? " answer
-    fi
-    if [ x${answer} = x ]; then
-	answer=${default}
-    fi
-    echo ${answer}
-}
-
-yesno() {
-    local dflt question answer
-
-    question=$1
-    dflt=$2
-    while :; do
-	answer=$(ask "${question}" "${dflt}")
-	case "${answer}" in
-	[Yy]*)		return 0;;
-	[Nn]*)		return 1;;
-	esac
-	echo "Please answer yes or no."
-    done
-}
-
-delete_account() {
-    local u g home
-
-    u=$1
-    g=$2
-    if yesno "Do you want me to remove group \"${g}\"" y; then
-	pw groupdel -n ${g}
-	echo "Done."
-    fi
-    if yesno "Do you want me to remove user \"${u}\"" y; then
-	eval home=~${u}
-	pw userdel -n ${u}
-	echo "Done."
-	if [ -d "${home}" ]; then
-	    echo "Please remember to remove the home directory \"${home}\""
-	fi
-    fi
-}
-
-if [ x$2 != xDEINSTALL ]; then
-    exit
-fi
-
-delete_account ${DNETFOLD_USER} ${DNETFOLD_GROUP}
diff --git a/biology/distribfold/pkg-descr b/biology/distribfold/pkg-descr
deleted file mode 100644
index 6e37a65754dc..000000000000
--- a/biology/distribfold/pkg-descr
+++ /dev/null
@@ -1,24 +0,0 @@
-[ excerpt from developer's site ]
-
-This is the distributedfolding.org's client. 
-
-It makes protein structures to help sample the enormous size of
-protein conformatoinal space. We hope to find a few good samples
-and understand how a large computation can help crack the problem
-of predicting protein structure - the protein folding problem.
-
-Proteins have a vast number of folds, larger than we could hope to
-compute even with distributed computing. Usually only one fold is
-found in nature. The Distributed Folding Project aims to test our
-new protein folding algorithm. We want see if it can reproduce
-natural protein folds after making extremely large samples of many
-different folds.
-
-With your help, we will create the largest samples of protein folds
-ever computed. First we will make 1 Billion (1,000,000,000) folds
-for 5 small proteins, then we will try 10 Billion (10,000,000,000)
-for another 10 large proteins. By the end of our first phase, we
-hope to make over 100 Billion protein folds spanning 15 different
-proteins.
-
-WWW: http://www.distributedfolding.org/
diff --git a/biology/distribfold/pkg-plist b/biology/distribfold/pkg-plist
deleted file mode 100644
index 868f34107dac..000000000000
--- a/biology/distribfold/pkg-plist
+++ /dev/null
@@ -1,28 +0,0 @@
-distribfold/cpu0/CompatibilityNotes.txt
-distribfold/cpu0/blpotential.txt
-distribfold/cpu0/bstdt.val
-distribfold/cpu0/cbdata
-distribfold/cpu0/copyright
-distribfold/cpu0/database.obs
-distribfold/cpu0/database.seq
-distribfold/cpu0/distrib-update
-distribfold/cpu0/foldit
-distribfold/cpu0/foldtrajlite
-distribfold/cpu0/native.val
-distribfold/cpu0/param19_eef1.inp
-distribfold/cpu0/phipsiwalk_dict.cdx
-distribfold/cpu0/phipsiwalk_dict.dbf
-distribfold/cpu0/phipsiwalk_dict.fpt
-distribfold/cpu0/protein.trj
-distribfold/cpu0/readme1st.txt
-distribfold/cpu0/rotlib.bin.bz2
-distribfold/cpu0/skel.prt
-distribfold/cpu0/solvpar.inp
-distribfold/cpu0/sspred.val
-distribfold/cpu0/toph19_eef1.inp
-distribfold/cpu0/whatsnew.txt
-distribfold/cpu0/zhangatm.txt
-distribfold/cpu0/zhangeij.txt
-@dirrmtry distribfold/cpu0
-etc/rc.d/distribfold.sh
-@unexec rmdir %D/distribfold 2>/dev/null || echo "If you are permanently removing this port, you should do a ``rm -rf ${PKG_PREFIX}/distribfold`` to remove any binary, configuration and log files left." | fmt
diff --git a/biology/kinemage/Makefile b/biology/kinemage/Makefile
deleted file mode 100644
index 2c11bd07ce54..000000000000
--- a/biology/kinemage/Makefile
+++ /dev/null
@@ -1,39 +0,0 @@
-# New ports collection Makefile for: kinemage
-# Date created:         Dec 4 1997
-# Whom:                 frankch@waru.life.nthu.edu.tw
-#
-# $FreeBSD$
-#
-
-PORTNAME=	kinemage
-PORTVERSION=	5.79
-PORTREVISION=	2
-CATEGORIES=	biology
-# There is no distfile to fetch here, just a dir of badly formatted sources
-#MASTER_SITES=	ftp://kinemage.biochem.duke.edu/OPEN_SOURCE/
-#MASTER_SITE_SUBDIR=	MAGE_001120
-# I've repackaged their sources for now and Will Andrews <will@freebsd.org>
-# is hosting
-MASTER_SITES=	${MASTER_SITE_LOCAL}
-MASTER_SITE_SUBDIR=	will
-DISTNAME=	mage-001120
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	A molecular visualization program with special functions
-
-DEPRECATED=	Looks like an abandonware, no more public distfile
-EXPIRATION_DATE=	2011-08-01
-
-USE_MOTIF=	YES
-
-ALL_TARGET=	mage
-PLIST_FILES=	bin/kinemage
-
-# When the time comes to use the actual master site, this snippet
-# will replace the carriage returns with newlines
-# perl -i -pe 's/\r/\n/g' ${WRKSRC}/*
-
-do-install:
-	@${INSTALL_PROGRAM} ${WRKSRC}/mage ${PREFIX}/bin/kinemage
-
-.include <bsd.port.mk>
diff --git a/biology/kinemage/distinfo b/biology/kinemage/distinfo
deleted file mode 100644
index 684a9723d0ff..000000000000
--- a/biology/kinemage/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (mage-001120.tar.gz) = 802be3c8f8641c4beadd7515a6aa0eed8d26933ad1e31b05c5b35f2de029fffc
-SIZE (mage-001120.tar.gz) = 511930
diff --git a/biology/kinemage/files/patch-Makefile b/biology/kinemage/files/patch-Makefile
deleted file mode 100644
index deb8db205d83..000000000000
--- a/biology/kinemage/files/patch-Makefile
+++ /dev/null
@@ -1,22 +0,0 @@
---- Makefile.orig	Mon Dec  4 20:47:11 2000
-+++ Makefile	Mon Dec  4 20:50:43 2000
-@@ -4,7 +4,7 @@
- # rpm -i ...rpm   (to install each in turn, where ...rpm is downloaded file
- # for Linux, try:                                                               
- # CFLAGS =  -I/usr/X11R6/LessTif/Motif2.0/include
--CFLAGS = -g  -I/usr/X11R6/LessTif/Motif2.0/include
-+CFLAGS += -I$(LOCALBASE)/include
- # for SGI use:
- # CFLAGS = -I/usr/include/X11
- # CFLAGS =  -g -I/usr/include/X11
-@@ -30,7 +30,9 @@
- # for linux with Motif installed, try:
- # LIBS = -L/usr/X11/lib -lXm -lXt -lX11
- # for Linux, try:
--LIBS = -L/usr/X11R6/LessTif/Motif2.0/lib -L/usr/X11R6/lib -lXm -lXt -lX11
-+# LIBS = -L/usr/X11R6/LessTif/Motif2.0/lib -L/usr/X11R6/lib -lXm -lXt -lX11
-+# For FreeBSD:
-+LIBS = -L$(LOCALBASE)/lib -lXm -lXt -lX11
- 
- # ------------------------------------------------------------------------
- 
diff --git a/biology/kinemage/pkg-descr b/biology/kinemage/pkg-descr
deleted file mode 100644
index 293e6e7215d6..000000000000
--- a/biology/kinemage/pkg-descr
+++ /dev/null
@@ -1,6 +0,0 @@
-Kinemage is a molecular visualization program. It is very suitable
-for educational usage.  This program is developed by David C.
-Richardson.  Kinemage stands for Kinetic Image.  The kinemage file
-can compose several molecules and descriptions.
-
-WWW: http://www.proteinscience.org/Kinemage/
diff --git a/biology/lsysexp/Makefile b/biology/lsysexp/Makefile
deleted file mode 100644
index 7bf81c314ee9..000000000000
--- a/biology/lsysexp/Makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-# New ports collection makefile for:	lsysexp
-# Date created:				22 Apr 2003
-# Whom:					David Yeske <dyeske@gmail.com>
-#
-# $FreeBSD$
-#
-
-PORTNAME=	lsysexp
-PORTVERSION=	0.67
-PORTREVISION=	11
-CATEGORIES=	biology
-MASTER_SITES=	http://coscorrosa.com/programs/${PORTNAME}/download/ \
-		http://freebsd.unixfreunde.de/sources/
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	A GTK based program for viewing and creating L-system fractals
-
-DEPRECATED=	Looks like an abandonware, no more public distfile
-EXPIRATION_DATE=	2011-08-01
-
-WRKSRC=		${WRKDIR}/lsysexp-0.67
-
-USE_GNOME=	gtk20
-GNU_CONFIGURE=	yes
-
-post-patch:
-	@${REINPLACE_CMD} -e \
-		's|-DGTK_DISABLE_DEPRECATED||' \
-		${WRKSRC}/src/Makefile.in
-
-.include <bsd.port.mk>
diff --git a/biology/lsysexp/distinfo b/biology/lsysexp/distinfo
deleted file mode 100644
index 1bae05e57d15..000000000000
--- a/biology/lsysexp/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (lsysexp-0.67.tar.gz) = 61e4fb9abcb0f9fd014d94e0358aeaf208856097bd9dca406de97e9eb1c03b7a
-SIZE (lsysexp-0.67.tar.gz) = 144512
diff --git a/biology/lsysexp/pkg-descr b/biology/lsysexp/pkg-descr
deleted file mode 100644
index a48f50d90d23..000000000000
--- a/biology/lsysexp/pkg-descr
+++ /dev/null
@@ -1,14 +0,0 @@
-L-system Explorer is a program used for viewing and creating L-system
-fractals.
-
-The following features are supported:
-
-- Over 500 builtin L-systems, arranged into about 20 groups.
-- Ability to create and save custom L-systems and L-system groups.
-- Abilty to save images of L-systems (in PNG or JPEG format).
-- Multiple L-systems can be viewed at the same time.
-- Able to use custom colors and gradients.
-- Can also generate random gradients, or completely random colors. 
-- Able to draw using lines, points, or a random combination of both.
-
-WWW: http://www.cs.pdx.edu/~coscorrr/programs/lsysexp/
diff --git a/biology/lsysexp/pkg-plist b/biology/lsysexp/pkg-plist
deleted file mode 100644
index 3e55ce66065b..000000000000
--- a/biology/lsysexp/pkg-plist
+++ /dev/null
@@ -1,30 +0,0 @@
-bin/lsysexp
-%%DATADIR%%/expand.pl
-%%DATADIR%%/fractint2lsysexp.pl
-%%DATADIR%%/icons/lsysexp-128x128.xpm
-%%DATADIR%%/icons/lsysexp-16x16.xpm
-%%DATADIR%%/icons/lsysexp-32x32.xpm
-%%DATADIR%%/icons/lsysexp-48x48.xpm
-%%DATADIR%%/icons/lsysexp-64x64.xpm
-%%DATADIR%%/lsysexp-help.html
-%%DATADIR%%/maps/Black-Red-Yellow.fmap
-%%DATADIR%%/maps/Blue-Cyan.fmap
-%%DATADIR%%/maps/Blue-Green.fmap
-%%DATADIR%%/maps/Blue-Slate.fmap
-%%DATADIR%%/maps/Blue-Yellow-Red.fmap
-%%DATADIR%%/maps/Caribbean-Blues.fmap
-%%DATADIR%%/maps/Cyan-Yellow.fmap
-%%DATADIR%%/maps/Deep-Sea.fmap
-%%DATADIR%%/maps/Full-Spectrum.fmap
-%%DATADIR%%/maps/Golden.fmap
-%%DATADIR%%/maps/Grayscale.fmap
-%%DATADIR%%/maps/Green-White-Red.fmap
-%%DATADIR%%/maps/Greens.fmap
-%%DATADIR%%/maps/Pastel-Rainbow.fmap
-%%DATADIR%%/maps/Red-White-Blue.fmap
-%%DATADIR%%/maps/Red-Yellow.fmap
-%%DATADIR%%/maps/Skyline.fmap
-%%DATADIR%%/maps/Yellow-Purple.fmap
-@dirrm %%DATADIR%%/maps
-@dirrm %%DATADIR%%/icons
-@dirrm %%DATADIR%%