academic/EMBASSY: Update binaries location.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 115 insertions, 74 deletions

diff --git a/academic/EMBASSY/EMBASSY.SlackBuild b/academic/EMBASSY/EMBASSY.SlackBuild
index d0049728d12c..337de5f778d4 100644
--- a/academic/EMBASSY/EMBASSY.SlackBuild
+++ b/academic/EMBASSY/EMBASSY.SlackBuild
@@ -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