diff options
| -rw-r--r-- | academic/EMBASSY/EMBASSY.SlackBuild | 189 |
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 |