mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-29 13:00:32 +01:00
141 lines
4.3 KiB
Bash
141 lines
4.3 KiB
Bash
#!/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}
|