Initial import of arka, version 0.11:

Arka is a program that serves as a graphical interface for the programs from
the GP package.

Furthermore, it has some interesting functions of it's own.  The main scope
of the program is the manipulation and visualisation of DNA / RNA / protein
sequences.

This package comes from pkgsrc-wip; created by <hdp at cs.nmsu.edu> with
several changes by me.

6 files changed, 101 insertions, 0 deletions

diff --git a/biology/arka/DESCR b/biology/arka/DESCR
new file mode 100644
index 00000000000..d5fa76b4423
--- /dev/null
+++ b/biology/arka/DESCR
@@ -0,0 +1,6 @@
+Arka is a program that serves as a graphical interface for the programs from
+the GP package.
+
+Furthermore, it has some interesting functions of it's own.  The main scope
+of the program is the manipulation and visualisation of DNA / RNA / protein
+sequences.
diff --git a/biology/arka/Makefile b/biology/arka/Makefile
new file mode 100644
index 00000000000..5774e08f39f
--- /dev/null
+++ b/biology/arka/Makefile
@@ -0,0 +1,41 @@
+# $NetBSD: Makefile,v 1.1.1.1 2005/03/27 13:08:45 jmmv Exp $
+#
+
+DISTNAME=	arka-0.11
+CATEGORIES= 	biology
+MASTER_SITES=	http://bioinformatics.org/genpak/download/
+EXTRACT_SUFX=	.tgz
+
+MAINTAINER=	hdp@cs.nmsu.edu
+HOMEPAGE=	http://www.bioinformatics.org/genpak/
+COMMENT=	Graphic interface for the programs from the GP package
+
+DEPENDS+=	gp-[0-9]*:../../biology/gp
+
+USE_DIRS+=	xdg-1.1
+USE_PKGINSTALL=	YES
+
+CONF_FILES=	${PREFIX}/share/examples/arka/arkarc ${PKG_SYSCONFDIR}/arkarc
+CPPFLAGS+=	-DARKA_GLOBAL=\"${PKG_SYSCONFDIR}/arkarc\"
+CPPFLAGS+=	-DARKA_PROGRAMS=\"${PKG_SYSCONFDIR}/arkarc\"
+
+INSTALLATION_DIRS=	bin man/man1
+
+post-build:
+	cd ${WRKSRC} && ${GUNZIP_CMD} arka.1.gz
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/arka ${PREFIX}/bin
+	${INSTALL_MAN} ${WRKSRC}/arka.1 ${PREFIX}/man/man1
+.for f in arka_16x16.xpm arka_32x32.xpm
+	${INSTALL_DATA} ${WRKSRC}/icons/${f} ${PREFIX}/share/pixmaps
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/arka
+.for f in CHANGES.TXT INSTALL.TXT LICENSE.TXT README.TXT TODO.TXT
+	${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/share/doc/arka
+.endfor
+	${INSTALL_DATA_DIR} ${PREFIX}/share/examples/arka
+	${INSTALL_DATA} ${WRKSRC}/arkarc ${PREFIX}/share/examples/arka
+
+.include "../../x11/gtk/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/arka/PLIST b/biology/arka/PLIST
new file mode 100644
index 00000000000..78344143409
--- /dev/null
+++ b/biology/arka/PLIST
@@ -0,0 +1,14 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2005/03/27 13:08:45 jmmv Exp $
+bin/arka
+man/man1/arka.1
+share/doc/arka/CHANGES.TXT
+share/doc/arka/INSTALL.TXT
+share/doc/arka/LICENSE.TXT
+share/doc/arka/README.TXT
+share/doc/arka/TODO.TXT
+share/examples/arka/arkarc
+share/pixmaps/arka_16x16.xpm
+share/pixmaps/arka_32x32.xpm
+@comment in xdg-dirs: @dirrm share/pixmaps
+@dirrm share/examples/arka
+@dirrm share/doc/arka
diff --git a/biology/arka/distinfo b/biology/arka/distinfo
new file mode 100644
index 00000000000..9245737244e
--- /dev/null
+++ b/biology/arka/distinfo
@@ -0,0 +1,7 @@
+$NetBSD: distinfo,v 1.1.1.1 2005/03/27 13:08:45 jmmv Exp $
+
+SHA1 (arka-0.11.tgz) = 7b1e373cb7e74a70da8c2c423dd6d7f3fecd6960
+RMD160 (arka-0.11.tgz) = 203d155b292cd34cd00f36b4162756081f03a6fc
+Size (arka-0.11.tgz) = 280123 bytes
+SHA1 (patch-aa) = 97321d794aa8dbe525ac50eb8f2409572485aa56
+SHA1 (patch-ab) = 935e3100a86cc6b43ff62a202f6337765a003c6a
diff --git a/biology/arka/patches/patch-aa b/biology/arka/patches/patch-aa
new file mode 100644
index 00000000000..736b206756d
--- /dev/null
+++ b/biology/arka/patches/patch-aa
@@ -0,0 +1,20 @@
+$NetBSD: patch-aa,v 1.1.1.1 2005/03/27 13:08:45 jmmv Exp $
+
+--- src/Makefile.orig	2001-05-09 22:28:41.000000000 +0200
++++ src/Makefile
+@@ -1,5 +1,5 @@
+ CC=gcc
+-CFLAGS=`gtk-config --cflags` -Wall
++CFLAGS+=$(CPPFLAGS) `gtk-config --cflags`
+ 
+ objects = komunikat.o main.o file.o interface.o genpak.o rcfile.o \
+ 	graph.o graph3d.o help.o programs.o options.o misc.o seqed.o search.o \
+@@ -10,7 +10,7 @@ all: arka
+ 	mv arka ..
+ 
+ arka:	$(objects)
+-	gcc -o arka $(objects)  `gtk-config --libs` -lm
++	gcc $(LDFLAGS) -o arka $(objects)  `gtk-config --libs` -lm
+ 
+ $(objects): main.h
+ 
diff --git a/biology/arka/patches/patch-ab b/biology/arka/patches/patch-ab
new file mode 100644
index 00000000000..0b29500a3ab
--- /dev/null
+++ b/biology/arka/patches/patch-ab
@@ -0,0 +1,13 @@
+$NetBSD: patch-ab,v 1.1.1.1 2005/03/27 13:08:45 jmmv Exp $
+
+--- src/options.c.orig	2001-05-04 15:36:12.000000000 +0200
++++ src/options.c
+@@ -50,7 +50,7 @@ int options_initialize(opt_s *opt) {
+ 	opt->command_history_size = 20 ;
+ 	opt->file_history_size = 5 ;
+ 
+-	opt->wdir = my_strdup(getenv("PWD")) ;
++	opt->wdir = getcwd(NULL, 0);
+ 	opt->wdir = realloc(opt->wdir, strlen(opt->wdir) + 2000) ;
+ 	strcat(opt->wdir, "/") ;
+