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#!/bin/sh
# Slackware build script for staden
# Copyright 2011-2012 Petar Petrov, ppetrov@paju.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.
PRGNAM=staden
VERSION=${VERSION:-2.0.0b9}
BUILD=${BUILD:-3}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i486 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
fi
SLKTCL=tcl8.6.1 # Slackware 14.1 sources for TCL
SLKTK=tk8.6.1 # Slackware 14.1 sources for TK
TKLIB=tklib0.5 # Folder name of TKLIB
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
mkdir $PRGNAM-$VERSION
cd $PRGNAM-$VERSION
tar xvf $CWD/$PRGNAM-$VERSION-src.tar.gz
tar xvf $CWD/${PRGNAM}_doc-$VERSION-src.tar.gz
# The sources of TCL and TK are expected to be in /tmp at build time,
# so we unpack them in the build directory and create symlinks in /tmp.
rm -f /tmp/$SLKTCL
rm -f /tmp/$SLKTK
tar xvf $CWD/$SLKTCL-src.tar.xz
tar xvf $CWD/$SLKTK-src.tar.xz
ln -s $TMP/$PRGNAM-$VERSION/$SLKTCL /tmp/$SLKTCL
ln -s $TMP/$PRGNAM-$VERSION/$SLKTK /tmp/$SLKTK
chown -R root:root $PRGNAM-$VERSION-src ${PRGNAM}_doc-$VERSION-src
find $PRGNAM-$VERSION-src ${PRGNAM}_doc-$VERSION-src \
\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
cd $PRGNAM-$VERSION-src
# On Slackware64, the components of staden (like GAP4, GAP5, PREGAP4,
# SPIN, TREV) will not run, as they still expect their libraries to be
# in /usr/lib not /usr/lib64. Let's correct the libraries path.
sed -i "s:$STADENROOT/lib:$STADENROOT/lib${LIBDIRSUFFIX}:g" \
global.mk staden.profile copy_reads/copy_reads gap4/gap4 gap5/gap5 \
gap5/gap5_consensus gap5/gap5_export gap5/tg_index gap5/tg_view \
prefinish/finish_sanger prefinish/prefinish pregap4/pregap4 spin/spin \
spin_emboss/create_emboss_files trev/trev
# Point to the right place of the EMBOSS .acd and data files. This is
# needed if the "create_emboss_files" script is run after install.
sed -i "133 c set acd_dir /usr/share/EMBOSS/acd" spin_emboss/create_emboss_files.tcl
sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin
# Correct the path where staden components look for their manual.
sed -i "s:/share/doc/staden/manual:/doc/$PRGNAM-$VERSION/manual:" tk_utils/help_config
# These fixes are from Arch linux AUR
# http://aur.archlinux.org/packages/st/staden/PKGBUILD
sed -i 's:-DSVN_VERSION=$(SVNVERS)::' system.mk.in
sed -i "s/gzFile\ \*gz/gzFile\ gz/" gap5/zfio.h
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--with-tklib=/usr/lib${LIBDIRSUFFIX}/$TKLIB \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build documentation. In the process, texi2dvi looks for tex and
# that's why the SlackBuild should be run as real root (su -).
# ## (or just source /etc/profile ) --rworkman
cd $TMP/$PRGNAM-$VERSION/${PRGNAM}_doc-$VERSION-src
# Fix the doc and man pages paths
sed "s:{datarootdir}/doc/staden:{prefix}/doc/$PRGNAM-$VERSION:" -i Makefile
sed "s:{datarootdir}/man:{prefix}/man:" -i Makefile
# Remove this, or there will be an error at the "make install" line.
rm -rf i/i
# Generate documentation. If you want it in the US letter format,
# change the next line to "make unix PAPER=us".
make unix
make install DESTDIR=$PKG
# Now that we're done building, let's remove those symlinks from earlier...
rm -f /tmp/$SLKTCL /tmp/$SLKTK
# This is empty
rm -rf $PKG/usr/share/doc
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/share/{applications,pixmaps}
cp $CWD/desktop/*.desktop $PKG/usr/share/applications
cp $CWD/desktop/*.png $PKG/usr/share/pixmaps
cd ../$PRGNAM-$VERSION-src
cp -a ChangeLog NEWS README.build $PKG/usr/doc/$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}
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