slackbuilds/academic/staden/staden.SlackBuild

#!/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 \
 \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
 -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}