mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-26 22:06:35 +01:00
fe3095faf8
I notified upstream that Staden had been added to SlackBuilds.org and got some handy tips. So: 1) The components of the program will now find their documentation directly. 2) The Staden package is now ready to provide a GUI for EMBOSS. 3) The real icons are used (converted from their Mac format). Signed-off-by: Robby Workman <rworkman@slackbuilds.org>
164 lines
5.6 KiB
Bash
164 lines
5.6 KiB
Bash
#!/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:-2}
|
|
TAG=${TAG:-_SBo}
|
|
|
|
if [ -z "$ARCH" ]; then
|
|
case "$( uname -m )" in
|
|
i?86) ARCH=i486 ;;
|
|
arm*) ARCH=arm ;;
|
|
*) ARCH=$( uname -m ) ;;
|
|
esac
|
|
fi
|
|
|
|
SLKTCL=tcl8.5.9 # Slackware 13.37 sources for TCL
|
|
SLKTK=tk8.5.9 # Slackware 13.37 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-$VERSION/manual:" tk_utils/help_config
|
|
|
|
CFLAGS="$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}
|