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academic/EMBASSY: Update binaries location.

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Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov 2022-07-29 22:21:46 +07:00 committed by Willy Sudiarto Raharjo
parent 32bfc419eb
commit fe51eaf70f
1 changed files with 115 additions and 74 deletions
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189
academic/EMBASSY/EMBASSY.SlackBuild
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@ -2,7 +2,7 @@
# Slackware build script for EMBASSY
# Copyright 2011-2021 Petar Petrov slackalaxy@gmail.com
# Copyright 2011-2022 Petar Petrov slackalaxy@gmail.com
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@ -26,7 +26,7 @@ cd $(dirname $0) ; CWD=$(pwd)
PRGNAM=EMBASSY
VERSION=${VERSION:-6.6.0} # Keep this the same version as EMBOSS
BUILD=${BUILD:-3}
BUILD=${BUILD:-4}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}
@ -64,6 +64,9 @@ else
LIBDIRSUFFIX=""
fi
# where to look for libraries
LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/EMBOSS"
# EMBASSY components and their versions
CBSTOOLS=CBSTOOLS-1.0.0.650
CLUSTALOMEGA=CLUSTALOMEGA-1.1.0
@ -122,11 +125,13 @@ find -L . \
# Build CBSTOOLS
cd $TMP/$PRGNAM-$VERSION/$CBSTOOLS
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
@ -137,240 +142,272 @@ make install DESTDIR=$PKG
# Build CLUSTALOMEGA
cd $TMP/$PRGNAM-$VERSION/$CLUSTALOMEGA
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/CLUSTALOMEGA \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build DOMAINATRIX
cd $TMP/$PRGNAM-$VERSION/$DOMAINATRIX
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/DOMAINATRIX \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build DOMALIGN
cd $TMP/$PRGNAM-$VERSION/$DOMALIGN
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/DOMALIGN \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build DOMSEARCH
cd $TMP/$PRGNAM-$VERSION/$DOMSEARCH
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/DOMSEARCH \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build EMNU
cd $TMP/$PRGNAM-$VERSION/$EMNU
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/EMNU \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build ESIM4
cd $TMP/$PRGNAM-$VERSION/$ESIM4
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/ESIM4 \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build HMMER
cd $TMP/$PRGNAM-$VERSION/$HMMER
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/HMMER \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build IPRSCAN
cd $TMP/$PRGNAM-$VERSION/$IPRSCAN
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/IPRSCAN \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build MEME
cd $TMP/$PRGNAM-$VERSION/$MEME
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MEME \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build MSE
cd $TMP/$PRGNAM-$VERSION/$MSE
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MSE \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build MYEMBOSS
cd $TMP/$PRGNAM-$VERSION/$MYEMBOSS
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSS \
--build=$ARCH-slackware-linux
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linuxx
make
make install DESTDIR=$PKG
# Build MYEMBOSSDEMO
cd $TMP/$PRGNAM-$VERSION/$MYEMBOSSDEMO
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSSDEMO \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build PHYLIPNEW
cd $TMP/$PRGNAM-$VERSION/$PHYLIPNEW
CFLAGS="$SLKCFLAGS -fcommon" \
CXXFLAGS="$SLKCFLAGS -fcommon" \
CFLAGS="$SLKCFLAGS -fcommon $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS -fcommon $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/PHYLIPNEW \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build SIGNATURE
cd $TMP/$PRGNAM-$VERSION/$SIGNATURE
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/SIGNATURE \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build STRUCTURE
cd $TMP/$PRGNAM-$VERSION/$STRUCTURE
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/STRUCTURE \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
# Build TOPO
cd $TMP/$PRGNAM-$VERSION/$TOPO
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
CFLAGS="$SLKCFLAGS $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/TOPO \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
@ -378,19 +415,23 @@ make install DESTDIR=$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" \
CFLAGS="$SLKCFLAGS -std=gnu89 $LIBDIRPATH" \
CXXFLAGS="$SLKCFLAGS -std=gnu89 $LIBDIRPATH" \
LDFLAGS="-L/usr/lib${LIBDIRSUFFIX}/EMBOSS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--libdir=/usr/lib${LIBDIRSUFFIX}/EMBOSS \
--bindir=/usr/lib${LIBDIRSUFFIX}/EMBOSS/bin \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/VIENNA \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make install DESTDIR=$PKG
mv $PKG/usr/share/PHYLIPNEW $PKG/usr/share/EMBOSS
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