[pkgsrc/trunk]: pkgsrc/biology/arka Initial import of arka, version 0.11:

[jmmv <jmmv%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/81506fae1af2
branches:  trunk
changeset: 491646:81506fae1af2
user:      jmmv <jmmv%pkgsrc.org@localhost>
date:      Sun Mar 27 13:08:45 2005 +0000

description:
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.

diffstat:

 biology/arka/DESCR            |   6 ++++++
 biology/arka/Makefile         |  41 +++++++++++++++++++++++++++++++++++++++++
 biology/arka/PLIST            |  14 ++++++++++++++
 biology/arka/distinfo         |   7 +++++++
 biology/arka/patches/patch-aa |  20 ++++++++++++++++++++
 biology/arka/patches/patch-ab |  13 +++++++++++++
 6 files changed, 101 insertions(+), 0 deletions(-)

diffs (125 lines):

diff -r 626739e02779 -r 81506fae1af2 biology/arka/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/arka/DESCR        Sun Mar 27 13:08:45 2005 +0000
@@ -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 -r 626739e02779 -r 81506fae1af2 biology/arka/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/arka/Makefile     Sun Mar 27 13:08:45 2005 +0000
@@ -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@localhost
+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 -r 626739e02779 -r 81506fae1af2 biology/arka/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/arka/PLIST        Sun Mar 27 13:08:45 2005 +0000
@@ -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 -r 626739e02779 -r 81506fae1af2 biology/arka/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/arka/distinfo     Sun Mar 27 13:08:45 2005 +0000
@@ -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 -r 626739e02779 -r 81506fae1af2 biology/arka/patches/patch-aa
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/arka/patches/patch-aa     Sun Mar 27 13:08:45 2005 +0000
@@ -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
+ 
+ $(objects): main.h
+ 
diff -r 626739e02779 -r 81506fae1af2 biology/arka/patches/patch-ab
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/arka/patches/patch-ab     Sun Mar 27 13:08:45 2005 +0000
@@ -0,0 +1,13 @@
+$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, "/") ;
+