academic/EMBASSY: Added (EMBOSS associated software)

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

5 files changed, 674 insertions, 0 deletions

diff --git a/academic/EMBASSY/CONTENTS b/academic/EMBASSY/CONTENTS
new file mode 100644
index 0000000000000..d739dcfb711ec
--- /dev/null
+++ b/academic/EMBASSY/CONTENTS
@@ -0,0 +1,94 @@
+The EMBASSY package includes the following:
+-------------------------------------------
+
+DOMAINATRIX Previous distributions of the protein domain programs from
+Jon Ison's group were in a single EMBASSY package. This is now split
+into 5 packages according to function.
+
+Application details and documentation for DOMAINATRIX
+
+DOMAINATRIX is available as a Beta release 0.1.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMAINATRIX-0.1.0.tar.gz
+
+Application details and documentation for DOMALIGN
+
+DOMALIGN is available as a Beta release 0.1.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMALIGN-0.1.0.tar.gz
+
+Application details and documentation for DOMSEARCH
+
+DOMSEARCH is available as a Beta release 0.1.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file DOMSEARCH-0.1.0.tar.gz
+
+Application details and documentation for SIGNATURE
+
+SIGNATURE is available as a Beta release 0.1.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file SIGNATURE-0.1.0.tar.gz
+
+Application details and documentation for STRUCTURE
+
+STRUCTURE is available as a Beta release 0.1.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file STRUCTURE-0.1.0.tar.gz EMNU
+(EMBOSS Menu is Not UNIX) Application details and documentation for EMNU
+
+EMNU is available as release 1.05 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file EMNU-1.05.tar.gz ESIM4
+(EMBOSS version of SIM4) Application details and documentation for ESIM4
+
+ESIM4 is available as release 1.0.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file ESIM4-1.0.0.tar.gz HMMER
+(EMBOSS version of HMMER 2.1.1 - PLEASE USE HMMERNEW) Application details
+and documentation for HMMER
+
+HMMER is available as release 2.1.1 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file HMMER-2.1.1.tar.gz HMMERNEW
+(EMBOSS version of HMMER 2.3.2) Application details and documentation
+for HMMERNEW
+
+HMMER 2.3.2 is available from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file HMMER-2.3.2.tar.gz
+MEME (previous EMBOSS version of MEME 2.3.1) Application details and
+documentation for MEME
+
+MEME is available as release 2.3.1 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file MEME-2.3.1.tar.gz MEMENEW
+(EMBOSS version of MEME 3.0.14) Application details and documentation
+for MEMENEW which wraps release 3.0.14 of the Meme package
+
+MEMENEW is available as release 0.1.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file MEMENEW-0.1.0.tar.gz
+MSE (A Multiple Sequence Screen Editor for Biological Sequences.)
+Application details and documentation for MSE
+
+MSE is available as release 1.0.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file MSE-1.0.0.tar.gz MYEMBOSS
+(For sites to build their own applications) Application details and
+documentation for MYEMBOSS
+
+MYEMBOSS provides a directory structure and makefile stubs for developing
+your own applications more easily than in versions before 3.0.0.
+
+MYEMBOSS requires autoconf, automake and libtool to be installed. See
+the INSTALL file for more informations.
+
+MYEMBOSS is available as release 1.0.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file MYEMBOSS-1.0.0.tar.gz PHYLIP
+(Phylogeny Inference Package) Application details and documentation for
+PHYLIP and PHYLIPNEW.
+
+PHYLIP 3.572 was available as an EMBASSY package with previous
+releases. From 3.0.0 we are including a beta test conversion of PHYLIP
+3.61 (PHYLIPNEW). Program names now begin with 'f' rather than 'e'
+and interfaces are more EMBOSS-like. Please pass on feedback to our bug
+reporting list emboss-bug@emboss.open-bio.org
+
+PHYLIPNEW is available as a Beta release 3.6b from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file PHYLIP-3.6b.tar.gz TOPO
+(Transmembrane display) Application details and documentation for TOPO
+
+TOPO is available as release 1.0.0 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file TOPO-1.0.0.tar.gz Vienna
+RNA package Application details and documentation for VIENNA
+
+Vienna is available as release 1.6 from our FTP server
+ftp://emboss.open-bio.org/pub/EMBOSS/ in file VIENNA-1.6.tar.gz
diff --git a/academic/EMBASSY/EMBASSY.SlackBuild b/academic/EMBASSY/EMBASSY.SlackBuild
new file mode 100644
index 0000000000000..6a4d1b27940cc
--- /dev/null
+++ b/academic/EMBASSY/EMBASSY.SlackBuild
@@ -0,0 +1,494 @@
+#!/bin/sh
+
+# Slackware build script for EMBASSY
+# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and 
+# hereby submitted to the public domain
+
+# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING 
+# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_ 
+# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
+
+PRGNAM=EMBASSY		
+VERSION=${VERSION:-6.4.0} # Keep this the same as the version of EMBOSS.
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}	
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i486 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+CWD=$(pwd)
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i486" ]; then
+  SLKCFLAGS="-O2 -march=i486 -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
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+mkdir $TMP/$PRGNAM-$VERSION
+
+# Build CBSTOOLS
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/CBSTOOLS-*.tar.gz 
+cd CBSTOOLS-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+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 DESTDIR=$PKG install
+
+# Build CLUSTALOMEGA
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/CLUSTALOMEGA-*.tar.gz
+cd CLUSTALOMEGA-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+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 DESTDIR=$PKG install
+
+# Build DOMAINATRIX
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/DOMAINATRIX-*.tar.gz
+cd DOMAINATRIX-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build DOMALIGN
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/DOMALIGN-*.tar.gz
+cd DOMALIGN-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build DOMSEARCH
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/DOMSEARCH-*.tar.gz
+cd DOMSEARCH-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build EMNU
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/EMNU-*.tar.gz
+cd EMNU-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build ESIM4
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/ESIM4-*.tar.gz
+cd ESIM4-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build HMMER
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/HMMER-*.tar.gz
+cd HMMER-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+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 DESTDIR=$PKG install
+
+# Build IPRSCAN
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/IPRSCAN-*.tar.gz
+cd IPRSCAN-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build MEME
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/MEME-*.tar.gz
+cd MEME-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build MSE
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/MSE-*.tar.gz
+cd MSE-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build MYEMBOSS
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/MYEMBOSS-*.tar.gz
+cd MYEMBOSS-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build MYEMBOSSDEMO
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/MYEMBOSSDEMO-*.tar.gz
+cd MYEMBOSSDEMO-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build PHYLIPNEW
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/PHYLIPNEW-*.tar.gz
+cd PHYLIPNEW-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+./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 DESTDIR=$PKG install
+
+# Build SIGNATURE
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/SIGNATURE-*.tar.gz
+cd SIGNATURE-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+
+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 DESTDIR=$PKG install
+
+# Build STRUCTURE
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/STRUCTURE-*.tar.gz
+cd STRUCTURE-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+
+# Build TOPO
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/TOPO-*.tar.gz
+cd TOPO-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;
+	
+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 DESTDIR=$PKG install
+	
+# Build VIENNA
+cd $TMP/$PRGNAM-$VERSION
+tar xvf $CWD/VIENNA-*.tar.gz
+cd VIENNA-*
+chown -R root:root .
+find . \
+ \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
+ -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
+ -exec chmod 644 {} \;	
+	
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+./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 DESTDIR=$PKG install
+
+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}
diff --git a/academic/EMBASSY/EMBASSY.info b/academic/EMBASSY/EMBASSY.info
new file mode 100644
index 0000000000000..b3175501f2bc6
--- /dev/null
+++ b/academic/EMBASSY/EMBASSY.info
@@ -0,0 +1,44 @@
+PRGNAM="EMBASSY"
+VERSION="6.4.0"
+HOMEPAGE="http://emboss.sourceforge.net/embassy/"
+DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/CLUSTALOMEGA-0.2.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/MEME-4.0.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/MYEMBOSS-6.4.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/MYEMBOSSDEMO-6.4.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/VIENNA-1.7.2.tar.gz"
+MD5SUM="2fe662f0af318cb8875bec734456286d \
+	c22e7669a6ca2cfa5c44e08774e69d88 \
+	06a46135fe82aa67d366f51a7228dc54 \
+	7ace7fb34d8f232e53006c8ba0efb7f5 \
+	f3deb5b13a3290ce2ca662561e279ea1 \
+	d39265e6143c961d2610c76693644fc4 \
+	f5cbcb0c04c8d61720a02ec5ff8200bb \
+	3d112bc9a22aa4e925a08fd9eee00485 \
+	4088463d7a84651e9b8693c97ca29428 \
+	3f221816b6db57b9a853b42985780ee9 \
+	faa80f5dcdd07751240853d3e34200e5 \
+	0e7aec2815857b71914f36873c14e71d \
+	a35ae3fd2ddd06f95f6ce82dca224b07 \
+	faa381608b65da74b990d4fc52e8c340 \
+	d8893c98eba597ae711a13cb588ecc2e \
+	911c621054c2ed147b5ac8d2e2230c9c \
+	c5132cc232fa930286fefc1241bc57c7 \
+	cc67545f95f15224926113a2bd3c38ad"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+MAINTAINER="Petar Petrov"
+EMAIL="ppetrov@paju.oulu.fi"
+APPROVED="Niels Horn"
diff --git a/academic/EMBASSY/README b/academic/EMBASSY/README
new file mode 100644
index 0000000000000..a147799664f5d
--- /dev/null
+++ b/academic/EMBASSY/README
@@ -0,0 +1,23 @@
+EMBASSY package includes applications with the same look and feel as 
+EMBOSS applications, but which the author wishes to be kept separate 
+from EMBOSS. This is usually because the packages are for specialised 
+sequence analysis or for non-sequence based analysis, or are licensed 
+differently to EMBOSS (i.e. non GPL).
+
+EMBASSY includes the following applications:
+
+- DOMAINATRIX
+- DOMALIGN
+- DOMSEARCH
+- PHYLIP
+- HMMER
+- EMNU
+- ESIM4
+- MEME
+- SIGNATURE
+- STRUCTURE
+- TOPO
+- MSE
+- VIENNA
+
+This requires EMBOSS.
diff --git a/academic/EMBASSY/slack-desc b/academic/EMBASSY/slack-desc
new file mode 100644
index 0000000000000..329780b6a13ed
--- /dev/null
+++ b/academic/EMBASSY/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.  Line
+# up the first '|' above the ':' following the base package name, and the '|'
+# on the right side marks the last column you can put a character in.  You must
+# make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':'.
+
+       |-----handy-ruler------------------------------------------------------|
+EMBASSY: EMBASSY (EMBOSS associated software)
+EMBASSY:
+EMBASSY: EMBASSY packages include applications with the same look and feel
+EMBASSY: as EMBOSS applications, but which the author wishes to be kept
+EMBASSY: separate from EMBOSS.
+EMBASSY:
+EMBASSY:
+EMBASSY:
+EMBASSY:
+EMBASSY:
+EMBASSY: Home: http://emboss.sourceforge.net/embassy/