path: root/academic/EMBASSY/EMBASSY.SlackBuild

#!/bin/bash

# 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}