academic/arka: Added (A GUI for genpak)

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

6 files changed, 156 insertions, 0 deletions

diff --git a/academic/arka/README b/academic/arka/README
new file mode 100644
index 0000000000000..e2f3dd43478d0
--- /dev/null
+++ b/academic/arka/README
@@ -0,0 +1,6 @@
+Arka is a program that serves as a graphical interface for the tools 
+from the GenPak (GP) package and has some interesting functions on 
+its own. Main scope of Arka is the manipulation and visualisation of 
+DNA / RNA / protein sequences.
+
+This requires genpak, available on SlackBuilds.org
diff --git a/academic/arka/arka.SlackBuild b/academic/arka/arka.SlackBuild
new file mode 100644
index 0000000000000..48ee14e6ed39a
--- /dev/null
+++ b/academic/arka/arka.SlackBuild
@@ -0,0 +1,97 @@
+#!/bin/sh
+
+# Slackware build script for arka
+# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and 
+# hereby submitted to the public domain
+
+# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING 
+# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ 
+# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
+
+PRGNAM=arka			
+VERSION=${VERSION:-0.11}	
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}		
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i486 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}	
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}	
+
+if [ "$ARCH" = "i486" ]; then
+  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+else
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+tar xvf $CWD/$PRGNAM-$VERSION.tgz
+cd $PRGNAM-$VERSION
+# Remove the pre-existing binary, just in case
+rm arka
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+# A few path fixes to the Makefile, although it will work anyways.
+sed "s:/usr/X11R6/bin:/usr/bin:" -i Makefile
+sed "s:/usr/X11R6/man:/usr/man:" -i Makefile
+sed "s:/usr/doc/packages:/usr/doc/arka-0.11:" -i Makefile
+sed "s:/usr/X11R6/include/X11/pixmaps:/usr/share/pixmaps:" -i Makefile
+
+# Use our CFLAGS
+sed -i "/^CFLAGS/s/=/+=/" src/Makefile
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+  make
+
+# The Makefile does not support "make DESTDIR install". So...
+install -D -m755 arka $PKG/usr/bin/arka
+install -D -m644 arkarc $PKG/etc/arkarc.new
+install -D -m644 arka.1.gz $PKG/usr/man/man1/arka.1.gz
+
+# Menu item and icon
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/arka.desktop $PKG/usr/share/applications
+cp ./icons/arka_100x100.xpm $PKG/usr/share/pixmaps/arka.xpm
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  README.TXT LICENSE.TXT CHANGES.TXT TODO.TXT \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+cat $CWD/doinst.sh > $PKG/install/doinst.sh
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
diff --git a/academic/arka/arka.desktop b/academic/arka/arka.desktop
new file mode 100644
index 0000000000000..3817a961aa76f
--- /dev/null
+++ b/academic/arka/arka.desktop
@@ -0,0 +1,6 @@
+[Desktop Entry]
+Categories=Education;
+Exec=arka
+Icon=arka.xpm
+Name=Arka GP
+Type=Application
diff --git a/academic/arka/arka.info b/academic/arka/arka.info
new file mode 100644
index 0000000000000..48683ac395050
--- /dev/null
+++ b/academic/arka/arka.info
@@ -0,0 +1,10 @@
+PRGNAM="arka"
+VERSION="0.11"
+HOMEPAGE="http://www.bioinformatics.org/genpak/"
+DOWNLOAD="http://www.bioinformatics.org/genpak/download/arka-0.11.tgz"
+MD5SUM="7cedbe3aeb7e71700beb6d4180f60f7c"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/arka/doinst.sh b/academic/arka/doinst.sh
new file mode 100644
index 0000000000000..72fe083ba0c93
--- /dev/null
+++ b/academic/arka/doinst.sh
@@ -0,0 +1,18 @@
+config() {
+  NEW="$1"
+  OLD="$(dirname $NEW)/$(basename $NEW .new)"
+  # If there's no config file by that name, mv it over:
+  if [ ! -r $OLD ]; then
+    mv $NEW $OLD
+  elif [ "$(cat $OLD | md5sum)" = "$(cat $NEW | md5sum)" ]; then
+    # toss the redundant copy
+    rm $NEW
+  fi
+  # Otherwise, we leave the .new copy for the admin to consider...
+}
+
+config etc/arkarc.new
+
+if [ -x /usr/bin/update-desktop-database ]; then
+  /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1
+fi
diff --git a/academic/arka/slack-desc b/academic/arka/slack-desc
new file mode 100644
index 0000000000000..59220170dbb70
--- /dev/null
+++ b/academic/arka/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.  Line
+# up the first '|' above the ':' following the base package name, and the '|'
+# on the right side marks the last column you can put a character in.  You must
+# make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':'.
+
+    |-----handy-ruler------------------------------------------------------|
+arka: arka (A GUI for genpak)
+arka:
+arka: Arka is a program that serves as a graphical interface for the
+arka: programs from the GenPak (GP) package and has some interesting
+arka: functions on its own.
+arka:
+arka:
+arka:
+arka:
+arka:
+arka: Home: http://www.bioinformatics.org/genpak/