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slackbuilds_ponce/academic/EMBASSY/EMBASSY.SlackBuild
Petar Petrov b29263e049
academic/EMBASSY: fix x86 arch and add -fcommon for PHYLIPNEW 
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
2021-05-18 23:40:03 +07:00

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#!/bin/sh
# Slackware build script for EMBASSY
# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com
# 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=EMBASSY
VERSION=${VERSION:-6.6.0} # Keep this the same version as EMBOSS
BUILD=${BUILD:-2}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
fi
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i586" ]; then
SLKCFLAGS="-O2 -march=i586 -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
# EMBASSY components and their versions
CBSTOOLS=CBSTOOLS-1.0.0.650
CLUSTALOMEGA=CLUSTALOMEGA-1.1.0
DOMAINATRIX=DOMAINATRIX-0.1.650
DOMALIGN=DOMALIGN-0.1.650
DOMSEARCH=DOMSEARCH-0.1.650
EMNU=EMNU-1.05.650
ESIM4=ESIM4-1.0.0.650
HMMER=HMMER-2.3.2.650
IPRSCAN=IPRSCAN-4.3.1.650
MEME=MEME-4.7.650
MSE=MSE-3.0.0.650
MYEMBOSS=MYEMBOSS-6.5.1
MYEMBOSSDEMO=MYEMBOSSDEMO-6.5.0
PHYLIPNEW=PHYLIPNEW-3.69.650
SIGNATURE=SIGNATURE-0.1.650
STRUCTURE=STRUCTURE-0.1.650
TOPO=TOPO-2.0.650
VIENNA=VIENNA-1.7.2.650
set -e
rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $PRGNAM-$VERSION
mkdir $TMP/$PRGNAM-$VERSION
cd $TMP/$PRGNAM-$VERSION
# Extract the components
tar xvf $CWD/$CBSTOOLS.tar.gz
tar xvf $CWD/$CLUSTALOMEGA.tar.gz
tar xvf $CWD/$DOMAINATRIX.tar.gz
tar xvf $CWD/$DOMALIGN.tar.gz
tar xvf $CWD/$DOMSEARCH.tar.gz
tar xvf $CWD/$EMNU.tar.gz
tar xvf $CWD/$ESIM4.tar.gz
tar xvf $CWD/$HMMER.tar.gz
tar xvf $CWD/$IPRSCAN.tar.gz
tar xvf $CWD/$MEME.tar.gz
tar xvf $CWD/$MSE.tar.gz
tar xvf $CWD/$MYEMBOSS.tar.gz
tar xvf $CWD/$MYEMBOSSDEMO.tar.gz
tar xvf $CWD/$PHYLIPNEW.tar.gz
tar xvf $CWD/$SIGNATURE.tar.gz
tar xvf $CWD/$STRUCTURE.tar.gz
tar xvf $CWD/$TOPO.tar.gz
tar xvf $CWD/$VIENNA.tar.gz
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 {} \;
# Build CBSTOOLS
cd $TMP/$PRGNAM-$VERSION/$CBSTOOLS
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build CLUSTALOMEGA
cd $TMP/$PRGNAM-$VERSION/$CLUSTALOMEGA
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/CLUSTALOMEGA \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build DOMAINATRIX
cd $TMP/$PRGNAM-$VERSION/$DOMAINATRIX
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/DOMAINATRIX \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build DOMALIGN
cd $TMP/$PRGNAM-$VERSION/$DOMALIGN
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/DOMALIGN \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build DOMSEARCH
cd $TMP/$PRGNAM-$VERSION/$DOMSEARCH
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/DOMSEARCH \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build EMNU
cd $TMP/$PRGNAM-$VERSION/$EMNU
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/EMNU \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build ESIM4
cd $TMP/$PRGNAM-$VERSION/$ESIM4
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/ESIM4 \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build HMMER
cd $TMP/$PRGNAM-$VERSION/$HMMER
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/HMMER \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build IPRSCAN
cd $TMP/$PRGNAM-$VERSION/$IPRSCAN
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/IPRSCAN \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build MEME
cd $TMP/$PRGNAM-$VERSION/$MEME
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MEME \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build MSE
cd $TMP/$PRGNAM-$VERSION/$MSE
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MSE \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build MYEMBOSS
cd $TMP/$PRGNAM-$VERSION/$MYEMBOSS
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build MYEMBOSSDEMO
cd $TMP/$PRGNAM-$VERSION/$MYEMBOSSDEMO
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSSDEMO \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build PHYLIPNEW
cd $TMP/$PRGNAM-$VERSION/$PHYLIPNEW
CFLAGS="$SLKCFLAGS -fcommon" \
CXXFLAGS="$SLKCFLAGS -fcommon" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/PHYLIPNEW \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build SIGNATURE
cd $TMP/$PRGNAM-$VERSION/$SIGNATURE
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/SIGNATURE \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build STRUCTURE
cd $TMP/$PRGNAM-$VERSION/$STRUCTURE
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/STRUCTURE \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build TOPO
cd $TMP/$PRGNAM-$VERSION/$TOPO
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/TOPO \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build VIENNA
cd $TMP/$PRGNAM-$VERSION/$VIENNA
# -std=gnu89 fixes build with gcc-5.2 (inline functions HairpinE and LoopEnergy)
CFLAGS="$SLKCFLAGS -std=gnu89" \
CXXFLAGS="$SLKCFLAGS -std=gnu89" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/VIENNA \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
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
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/CONTENTS > $PKG/usr/doc/$PRGNAM-$VERSION/CONTENTS
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}
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