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
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
|
#!/bin/sh
# Slackware build script for PhyML
# Copyright 2011-2017 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.
# Thanks to Niels Horn for some handy modifications and corrections.
PRGNAM=PhyML
SRCNAM=$(echo $PRGNAM | tr A-Z a-z)
VERSION=${VERSION:-3.3.20170530}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
fi
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i586" ]; then
SLKCFLAGS="-O2 -march=i586 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$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 $SRCNAM-$VERSION
tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
cd $SRCNAM-$VERSION
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 \
\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
# This is PhyML, the main component of the package. If this is all you want, you
# can comment out the sections that build PhyML MPI and Phyrex below.
./autogen.sh
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--enable-phyml \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
# Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" src/Makefile
sed -i "/^CFLAGS/s/=/+=/" Makefile
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
make
make install DESTDIR=$PKG
# This is PhyML MPI. If you do not want it, comment the lines below. Then you do
# not need to install openmpi.
./autogen.sh
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--enable-mpi \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
# Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" src/Makefile
sed -i "/^CFLAGS/s/=/+=/" Makefile
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
make
make install DESTDIR=$PKG
# This is Phyrex
./autogen.sh
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--enable-phyrex \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
# Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" src/Makefile
sed -i "/^CFLAGS/s/=/+=/" Makefile
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
make
make install DESTDIR=$PKG
# This is PhyTime
./autogen.sh
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--enable-phytime \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--build=$ARCH-slackware-linux
# Use our CFLAGS
sed -i "/^CFLAGS/s/=/+=/" src/Makefile
sed -i "/^CFLAGS/s/=/+=/" Makefile
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
make
make install DESTDIR=$PKG
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
# Include some examples
mkdir -p $PKG/usr/share/$PRGNAM
cp -a \
examples/{lg4x,phyrex_input_files,nexus_example.nxs,nucleic,proteic} \
$PKG/usr/share/$PRGNAM
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
doc/$SRCNAM-manual.pdf AUTHORS ChangeLog COPYING LICENSE README \
$PKG/usr/doc/$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
cd $PKG
/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
|
