11 files changed, 146 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index c66e42a81840..5be076006729 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -2,6 +2,7 @@
 #
 
     SUBDIR += artemis
+    SUBDIR += avida
     SUBDIR += babel
     SUBDIR += biojava
     SUBDIR += chemeq
diff --git a/biology/avida/Makefile b/biology/avida/Makefile
new file mode 100644
index 000000000000..d02462e1fd4f
--- /dev/null
+++ b/biology/avida/Makefile
@@ -0,0 +1,39 @@
+# New ports collection makefile for:	avida
+# Date created:		17 April 2002
+# Whom:			Jeremy <karlj000@unbc.ca>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	avida
+PORTVERSION=	1.6.0
+CATEGORIES=	biology
+MASTER_SITES=	http://dllab.caltech.edu/avida/versions/
+
+MAINTAINER=	karlj000@unbc.ca
+
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION:C/\.[[:alnum:]]+$//}
+USE_GMAKE=	yes
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--enable-viewer --enable-standard-prefix --prefix=${PREFIX} --datadir=${PREFIX}/share/${PORTNAME}
+
+post-patch:
+	# Change source/defs.hh prefix and port name.
+	@ ${MV} ${WRKSRC}/source/defs.hh ${WRKSRC}/source/defs.hh.presed
+	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#g' ${WRKSRC}/source/defs.hh.presed \
+	| ${SED} -e 's#%%PORTNAME%%#${PORTNAME}#g' \
+	> ${WRKSRC}/source/defs.hh
+
+	# Change source/support/genesis prefix and port name.
+	@ ${MV} ${WRKSRC}/source/support/genesis ${WRKSRC}/source/support/genesis.presed
+	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#g' ${WRKSRC}/source/support/genesis.presed \
+	| ${SED} -e 's#%%PORTNAME%%#${PORTNAME}#g' \
+	> ${WRKSRC}/source/support/genesis
+
+	# Change source/support/genesis.heads prefix and port name.
+	@ ${MV} ${WRKSRC}/source/support/genesis.heads ${WRKSRC}/source/support/genesis.heads.presed
+	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#g' ${WRKSRC}/source/support/genesis.heads.presed \
+	| ${SED} -e 's#%%PORTNAME%%#${PORTNAME}#g' \
+	> ${WRKSRC}/source/support/genesis.heads
+
+.include <bsd.port.mk>
diff --git a/biology/avida/distinfo b/biology/avida/distinfo
new file mode 100644
index 000000000000..d0e179ea3e42
--- /dev/null
+++ b/biology/avida/distinfo
@@ -0,0 +1 @@
+MD5 (avida-1.6.0.tar.gz) = 2294af061f200c486de2ed889e0e17af
diff --git a/biology/avida/files/patch-aa b/biology/avida/files/patch-aa
new file mode 100644
index 000000000000..554cac9efe93
--- /dev/null
+++ b/biology/avida/files/patch-aa
@@ -0,0 +1,10 @@
+--- source/event/event_base.hh.orig	Wed Apr 17 21:26:31 2002
++++ source/event/event_base.hh	Wed Apr 17 21:26:41 2002
+@@ -18,6 +18,7 @@
+ 
+ #include "../defs.hh"
+ #include <values.h>
++#include <float.h>
+ //#include "event_defs.hh"
+ 
+ enum eTriggerVariable { UPDATE, GENERATION, IMMEDIATE, UNDEFINED };
diff --git a/biology/avida/files/patch-ab b/biology/avida/files/patch-ab
new file mode 100644
index 000000000000..453635356a94
--- /dev/null
+++ b/biology/avida/files/patch-ab
@@ -0,0 +1,10 @@
+--- source/main/fitness_matrix.hh.orig	Thu Apr 18 08:54:04 2002
++++ source/main/fitness_matrix.hh	Thu Apr 18 08:54:15 2002
+@@ -7,6 +7,7 @@
+ #include <vector>
+ #include <map>
+ #include <list>
++#include <sys/types.h>
+ #include <sys/timeb.h>
+ 
+ #include "../cpu/cpu.hh"
diff --git a/biology/avida/files/patch-ac b/biology/avida/files/patch-ac
new file mode 100644
index 000000000000..980deaebc657
--- /dev/null
+++ b/biology/avida/files/patch-ac
@@ -0,0 +1,11 @@
+--- source/defs.hh.orig	Thu Apr 18 18:42:56 2002
++++ source/defs.hh	Thu Apr 18 18:43:14 2002
+@@ -8,7 +8,7 @@
+ #ifndef DEFS_HH
+ #define DEFS_HH
+ 
+-#define DEFAULT_DIR "../work/"
++#define DEFAULT_DIR "%%PREFIX%%/share/%%PORTNAME%%/"
+ 
+ // -= Remove bugfixes that change execution
+ //#define REMOVE_SIZE_RANGE_FIX      // had only affected upper limit in heads
diff --git a/biology/avida/files/patch-ad b/biology/avida/files/patch-ad
new file mode 100644
index 000000000000..0440d2e48130
--- /dev/null
+++ b/biology/avida/files/patch-ad
@@ -0,0 +1,11 @@
+--- source/support/genesis.orig	Fri Apr 19 20:00:53 2002
++++ source/support/genesis	Fri Apr 19 20:02:24 2002
+@@ -13,7 +13,7 @@
+ RANDOM_SEED 0		# Random number seed. (0 for based on time)
+ 
+ ### Configuration Files ###
+-DEFAULT_DIR ../work/         # Directory in which config files can be found.
++DEFAULT_DIR %%PREFIX%%/share/%%PORTNAME%%/ # Directory in which config files can be found.
+ INST_SET inst_set.28.base    # File containing instruction set.
+ TASK_SET task_set            # File containing task set.
+ RESOURCE_SET resource_set    # File containing resource set.
diff --git a/biology/avida/files/patch-ae b/biology/avida/files/patch-ae
new file mode 100644
index 000000000000..34a692b7cbca
--- /dev/null
+++ b/biology/avida/files/patch-ae
@@ -0,0 +1,11 @@
+--- source/support/genesis.heads.orig	Fri Apr 19 20:01:09 2002
++++ source/support/genesis.heads	Fri Apr 19 20:02:47 2002
+@@ -13,7 +13,7 @@
+ RANDOM_SEED 0		# Random number seed. (0 for based on time)
+ 
+ ### Configuration Files ###
+-DEFAULT_DIR ../work/         # Directory in which config files can be found.
++DEFAULT_DIR %%PREFIX%%/share/%%PORTNAME%%/ # Directory in which config files can be found.
+ INST_SET inst_set.26.heads.new    # File containing instruction set.
+ TASK_SET task_set            # File containing task set.
+ RESOURCE_SET resource_set            # File containing resource set.
diff --git a/biology/avida/pkg-comment b/biology/avida/pkg-comment
new file mode 100644
index 000000000000..7d166f5a2674
--- /dev/null
+++ b/biology/avida/pkg-comment
@@ -0,0 +1 @@
+Avida is an auto-adaptive genetic system designed for ALife research
diff --git a/biology/avida/pkg-descr b/biology/avida/pkg-descr
new file mode 100644
index 000000000000..3f85f3975c88
--- /dev/null
+++ b/biology/avida/pkg-descr
@@ -0,0 +1,16 @@
+The computer program avida is an auto-adaptive genetic system designed
+primarily for use as a platform in Digital or Artificial Life research. The
+avida system is based on concepts similar to those employed by the tierra
+program developed by Tom Ray. It is a population of self-reproducing strings
+with a Turing-complete genetic basis subjected to Poisson-random mutations.
+The population adapts to the combination of an intrinsic fitness landscape
+(self-reproduction) and an externally imposed (extrinsic) fitness function
+provided by the researcher. By studying this system, one can examine
+evolutionary adaptation, general traits of living systems (such as
+self-organization), and other issues pertaining to theoretical or
+evolutionary biology and dynamic systems.
+
+WWW: http://dllab.caltech.edu/avida/
+
+Jeremy
+karlj000@unbc.ca
diff --git a/biology/avida/pkg-plist b/biology/avida/pkg-plist
new file mode 100644
index 000000000000..e7ce0d5f69bd
--- /dev/null
+++ b/biology/avida/pkg-plist
@@ -0,0 +1,35 @@
+bin/avida
+share/avida/creature.base
+share/avida/creature.heads
+share/avida/creature.heads.new
+share/avida/genesis
+share/avida/genesis.heads
+share/avida/inst_set.19.short
+share/avida/inst_set.24.base
+share/avida/inst_set.26.heads.new
+share/avida/inst_set.27.multi
+share/avida/inst_set.27.no-nop
+share/avida/inst_set.27.parasite
+share/avida/inst_set.28.base
+share/avida/inst_set.28.const
+share/avida/inst_set.28.dir-match
+share/avida/inst_set.29.base_memsize
+share/avida/inst_set.31.multi
+share/avida/inst_set.32.heads
+share/avida/inst_set.84.long
+share/avida/inst_set.args
+share/avida/inst_set.big
+share/avida/inst_set.dev
+share/avida/inst_set.full
+share/avida/inst_set.long
+share/avida/inst_set.re
+share/avida/inst_set.red
+share/avida/inst_set.short
+share/avida/inst_set.test
+share/avida/inst_set.tiny
+share/avida/inst_set.travc
+share/avida/event_list
+share/avida/resource_set
+share/avida/task_set
+share/avida/analyze.cfg
+@dirrm share/avida