aboutsummaryrefslogtreecommitdiff
path: root/academic/samtools/samtools.SlackBuild
blob: a3c0e2d1a7d5af5ade5e28fc7a74463df577e8f9 (plain)
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
#!/bin/sh

# Slackware build script for samtools

# Copyright 2013 Petar Petrov, petar.petrov@student.oulu.fi
# 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 about the install paths from Arch Linux AUR:
# https://aur.archlinux.org/packages/sa/samtools/PKGBUILD

PRGNAM=samtools	
VERSION=${VERSION:-0.1.19}
BUILD=${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.tar.bz2
cd $PRGNAM-$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 {} \;

# Use our CFLAGS/CXXFLAGS
sed -i "/^C.*.*FLAGS/s/=/+=/" Makefile

CFLAGS="$SLKCFLAGS" \
make
make razip

# Install samtools, razip and bam library
install -D -m755 samtools $PKG/usr/bin/samtools
install -D -m755 razip	  $PKG/usr/bin/razip
install -D -m644 libbam.a $PKG/usr/lib${LIBDIRSUFFIX}/libbam.a

# Install bcftools its library and vsfutils
cd bcftools
install -D -m755 bcftools $PKG/usr/bin/bcftools
install -D -m644 libbcf.a $PKG/usr/lib${LIBDIRSUFFIX}/libbcf.a
install -D -m755 vcfutils.pl $PKG/usr/bin/vcfutils.pl

# Include additional executables
cd ../misc
install -D -m755 ace2sam	$PKG/usr/libexec/$PRGNAM/ace2sam
install -D -m755 bamcheck	$PKG/usr/libexec/$PRGNAM/bamcheck
install -D -m755 maq2sam-long	$PKG/usr/libexec/$PRGNAM/maq2sam-long
install -D -m755 maq2sam-short	$PKG/usr/libexec/$PRGNAM/maq2sam-short
install -D -m755 md5fa		$PKG/usr/libexec/$PRGNAM/md5fa
install -D -m755 md5sum-lite	$PKG/usr/libexec/$PRGNAM/md5sum-lite
install -D -m755 wgsim		$PKG/usr/libexec/$PRGNAM/wgsim

# Include some scripts
mkdir -p $PKG/usr/share/$PRGNAM
cp -a \
  *.pl *.lua *.py plot-bamcheck \
  $PKG/usr/share/$PRGNAM

# Include bam header files
cd ..
mkdir -p  $PKG/usr/include/bam
 for f in *.h ; do
   install -m644 $f "$PKG/usr/include/bam"
 done

# Install manpage
install -D -m644 $PRGNAM.1 $PKG/usr/man/man1/$PRGNAM.1

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

find $PKG/usr/man -type f -exec gzip -9 {} \;
for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done

mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
  AUTHORS COPYING INSTALL NEWS \
  $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References

# Fix permissions in the package...
find $PKG/usr/{doc,include,share} \
-type d -exec chmod 755 {} \; -o \
-type f -exec chmod 644 {} \;

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}