#!/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}