1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
|
#!/bin/bash
# Slackware build script for clustalx
# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
# permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# With help from http://aur.archlinux.org/packages.php?ID=25080
# PKGBUILD submitter is mickelliot and maintainer is machoo02
cd $(dirname $0) ; CWD=$(pwd)
PRGNAM=clustalx
VERSION=${VERSION:-2.1}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) export ARCH=i486 ;;
arm*) export ARCH=arm ;;
*) export ARCH=$( uname -m ) ;;
esac
fi
# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
# the name of the created package would be, and then exit. This information
# could be useful to other scripts.
if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
exit 0
fi
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 patches are from Archlinux AUR, as mentioned above.
patch -p1 < $CWD/fix-static.patch
patch -p1 < $CWD/QT.patch
chown -R root:root .
find -L . \
\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-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
|
