academic/clustalx: Added (Multiple Sequence Alignment GUI)

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

1 files changed, 104 insertions, 0 deletions

diff --git a/academic/clustalx/clustalx.SlackBuild b/academic/clustalx/clustalx.SlackBuild
new file mode 100644
index 0000000000..4505745095
--- /dev/null
+++ b/academic/clustalx/clustalx.SlackBuild
@@ -0,0 +1,104 @@
+#!/bin/sh
+
+# Slackware build script for clustalx
+# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and 
+# hereby submitted to the public domain
+
+# Based on the clustalx PKGBUILD from Archlinux AUR 
+# (http://aur.archlinux.org/packages.php?ID=25080). 
+# PKGBUILD submitter is mickelliot and maintainer is 
+# machoo02. Thank you!
+
+# 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=clustalx
+VERSION=${VERSION:-2.1}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) export ARCH=i486 ;;
+    arm*) export ARCH=arm ;;
+       *) export ARCH=$( 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.tar.gz
+cd $PRGNAM-$VERSION
+
+# The patch is from Archlinux AUR, as mentioned above.
+patch -p1 < $CWD/fix-static.patch
+
+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 {} \;
+
+sed -i 's/static//g' clustalx.pro
+
+qmake
+
+#Use our CFLAGS/CXXFLAGS
+sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+  make
+
+install -D -m755 clustalx $PKG/usr/bin/clustalx
+install -D -m644 colprot.xml $PKG/usr/share/$PRGNAM/colprot.xml
+install -D -m644 coldna.xml $PKG/usr/share/$PRGNAM/coldna.xml
+install -D -m644 coldna.xml $PKG/usr/share/$PRGNAM/colprint.xml
+install -D -m644 clustalx.hlp $PKG/usr/share/$PRGNAM/clustalx.hlp
+
+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
+
+# Menu item and icon
+mkdir -p $PKG/usr/share/{applications,pixmaps}
+cp $CWD/clustalx.desktop $PKG/usr/share/applications
+cp $CWD/clustalx.png $PKG/usr/share/pixmaps
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  README COPYING \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
+
+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}