acacemic/EMBASSY: Updated for version 6.5.7.

Signed-off-by: Robby Workman <rworkman@slackbuilds.org>

5 files changed, 195 insertions, 324 deletions

diff --git a/academic/EMBASSY/CONTENTS b/academic/EMBASSY/CONTENTS
index d739dcfb711e..bd0665b82b44 100644
--- a/academic/EMBASSY/CONTENTS
+++ b/academic/EMBASSY/CONTENTS
@@ -1,94 +1,64 @@
-The EMBASSY package includes the following:
--------------------------------------------
+CBSTOOLS: The CBSTOOLS package is a set of wrappers to selected
+applications from the CBS group in Denmark.
 
-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.
+CLUSTALOMEGA: A wrapper for the clustal omega application.
 
-Application details and documentation for DOMAINATRIX
+DOMAINATRIX: The DOMAINATRIX programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-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
+DOMALIGN: The DOMALIGN programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-Application details and documentation for DOMALIGN
+DOMSEARCH: The DOMSEARCH programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-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
+EMNU: The EMNU package is a simple EMBOSS menu system written by Gary
+Williams at HGMP.
 
-Application details and documentation for DOMSEARCH
+ESIM4: The ESIM4 package is an EMBOSS conversion of the SIM4 package
+from Liliana Florea.
 
-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
+HMMER: A suite of application wrappers to the original hmmer v2.3.2
+applications written by Sean Eddy. hmmer v2.3.2 must be installed on
+the same system as EMBOSS and the location of the hmmer executables
+must be defined in your path for EMBASSY HMMER to work.
 
-Application details and documentation for SIGNATURE
+IPRSCAN: The IPRSCAN package is a wrapper for the interproscan
+program.
 
-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
+MEME: The EMBASSY MEME package contains 'wrapper' applications
+providing an EMBOSS-style interface to the applications in the
+original MEME package version 4.0.0 developed by Timothy L. Bailey.
 
-Application details and documentation for STRUCTURE
+MIRA: The MIRA package is a fragment assembly program from Bastien
+Chevreux. The program was converted to EMBOSS by Alan Bleasby as two
+applications, one for EST assembly and one for shotgun fragment
+assembly
 
-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
+MSE: The MSE package is a multiple sequence editor. The program was
+contributed to the EMBOSS package by the author, Will Gilbert, as one
+of the first EMBASSY programs.
 
-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
+MYEMBOSS: A package for your own software developments.
 
-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
+MYEMBOSSDEMO: The MYEMBOSSDEMO package contains example applications
+using EMBOSS data types
 
-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
+PHYLIPNEW: The PHYLIPNEW programs are EMBOSS conversions of the
+programs in Joe Felsenstein's PHYLIP package, version 3.69.
 
-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
+SIGNATURE: The SIGNATURE programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-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
+STRUCTURE: The STRUCTURE programs were developed by Jon Ison and
+colleagues at MRC HGMP for their protein domain research. They are
+included as an EMBASSY package as a work in progress.
 
-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
+TOPO: The TOPO package is a graphics program to display membrane
+protein topology by Susan Jean Johns.
 
-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
+VIENNA: These programs are adapted from the VIENNA RNA package.
diff --git a/academic/EMBASSY/EMBASSY.SlackBuild b/academic/EMBASSY/EMBASSY.SlackBuild
index 6a4d1b27940c..eb67a7adcfe6 100644
--- a/academic/EMBASSY/EMBASSY.SlackBuild
+++ b/academic/EMBASSY/EMBASSY.SlackBuild
@@ -1,17 +1,31 @@
 #!/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=${VERSION:-6.4.0} # Keep this the same as the version of EMBOSS.
+# Copyright 2011-2012  Petar Petrov, ppetrov@paju.oulu.fi
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE
+
+PRGNAM=EMBASSY
+VERSION=${VERSION:-6.5.7} # Keep this the same version as EMBOSS
 BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}	
+TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
@@ -40,6 +54,26 @@ else
   LIBDIRSUFFIX=""
 fi
 
+# EMBASSY components and their versions
+CBSTOOLS=CBSTOOLS-1.0.0.650
+CLUSTALOMEGA=CLUSTALOMEGA-0.2.0.650
+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
@@ -47,11 +81,28 @@ 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-*
+
+# 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 . \
  \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
@@ -59,6 +110,8 @@ find . \
  \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
  -exec chmod 644 {} \;
 
+# Build CBSTOOLS
+cd $TMP/$PRGNAM-$VERSION/$CBSTOOLS
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -68,21 +121,12 @@ CXXFLAGS="$SLKCFLAGS" \
   --localstatedir=/var \
   --mandir=/usr/man \
   --docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
-  --build=$ARCH-slackware-linux 
+  --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-
+cd $TMP/$PRGNAM-$VERSION/$CLUSTALOMEGA
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -94,19 +138,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/CLUSTALOMEGA \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$DOMAINATRIX
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -118,19 +153,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/DOMAINATRIX \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$DOMALIGN
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -142,19 +168,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/DOMALIGN \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$DOMSEARCH
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -166,19 +183,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/DOMSEARCH \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$EMNU
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -190,19 +198,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/EMNU \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$ESIM4
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -214,19 +213,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/ESIM4 \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-
+cd $TMP/$PRGNAM-$VERSION/$HMMER
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -238,19 +228,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/HMMER \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$IPRSCAN
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -262,19 +243,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/IPRSCAN \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$MEME
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -286,19 +258,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/MEME \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$MSE
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -310,19 +273,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/MSE \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$MYEMBOSS
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -334,19 +288,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSS \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$MYEMBOSSDEMO
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -358,19 +303,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSSDEMO \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-
+cd $TMP/$PRGNAM-$VERSION/$PHYLIPNEW
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -382,19 +318,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/PHYLIPNEW \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-
+cd $TMP/$PRGNAM-$VERSION/$SIGNATURE
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -406,19 +333,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/SIGNATURE \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$STRUCTURE
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -430,19 +348,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/STRUCTURE \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$PKG
 
 # 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 {} \;
-	
+cd $TMP/$PRGNAM-$VERSION/$TOPO
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -454,19 +363,10 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/TOPO \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
-	
+make install DESTDIR=$PKG
+
 # 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 {} \;	
-	
+cd $TMP/$PRGNAM-$VERSION/$VIENNA
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -478,7 +378,7 @@ CXXFLAGS="$SLKCFLAGS" \
   --docdir=/usr/doc/$PRGNAM-$VERSION/VIENNA \
   --build=$ARCH-slackware-linux
 make
-make DESTDIR=$PKG install
+make install DESTDIR=$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
diff --git a/academic/EMBASSY/EMBASSY.info b/academic/EMBASSY/EMBASSY.info
index 65685dce3c65..49623f8ba1c2 100644
--- a/academic/EMBASSY/EMBASSY.info
+++ b/academic/EMBASSY/EMBASSY.info
@@ -1,42 +1,42 @@
 PRGNAM="EMBASSY"
-VERSION="6.4.0"
+VERSION="6.5.7"
 HOMEPAGE="http://emboss.sourceforge.net/embassy/"
-DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/CBSTOOLS-1.0.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/CLUSTALOMEGA-0.2.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/DOMAINATRIX-0.1.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/DOMALIGN-0.1.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/DOMSEARCH-0.1.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/EMNU-1.05.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/ESIM4-1.0.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/HMMER-2.3.2.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/IPRSCAN-4.3.1.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/MEME-4.0.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/MSE-3.0.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/MYEMBOSS-6.4.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/MYEMBOSSDEMO-6.4.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/PHYLIPNEW-3.69.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/SIGNATURE-0.1.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/STRUCTURE-0.1.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/TOPO-2.0.0.tar.gz \
-	ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/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="ftp://emboss.open-bio.org/pub/EMBOSS/CBSTOOLS-1.0.0.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/CLUSTALOMEGA-0.2.0.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-0.1.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/DOMALIGN-0.1.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/DOMSEARCH-0.1.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/EMNU-1.05.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/ESIM4-1.0.0.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/HMMER-2.3.2.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/IPRSCAN-4.3.1.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/MEME-4.7.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/MSE-3.0.0.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/MYEMBOSS-6.5.1.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/MYEMBOSSDEMO-6.5.0.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/SIGNATURE-0.1.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/STRUCTURE-0.1.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/TOPO-2.0.650.tar.gz \
+	ftp://emboss.open-bio.org/pub/EMBOSS/VIENNA-1.7.2.650.tar.gz"
+MD5SUM="4913776ee5ff93ae839762107f8d8bc8 \
+f24967741eb2fe9c3bccd6458276e127 \
+d7539f6ee6f25bb401ffad2802441010 \
+079a6371390201fa39f19c25cce8d5ba \
+5fd0e943f4db9f9ea008eabd68dc60e7 \
+6e0b7ac797554c52f413d23e5781e71b \
+2ca9069bf9c87697bf52c77b25a659d7 \
+d82017cc68ce3d381e8cc6dcfd68f39e \
+81720978302afc8d855b316651be5b2a \
+4d2dac5a2d66ad43552271be81c1cd1b \
+3b26ecbdf8032680f1de148f5d91d776 \
+54e9ca4dadd0b988f8964f886c6f026c \
+f3cb3421a79e7e6466686628de346b20 \
+488d117d32a391a9b53c60260595e67b \
+361773a6f1b0b862f5cbf3d4d3ee1fa0 \
+40afa99f995f34275005b76f8b05c337 \
+5a0b0c478cece42cc564599b91f9c1cf \
+633c16e28818b0dc4d3ae084a7beae56"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="EMBOSS"
diff --git a/academic/EMBASSY/README b/academic/EMBASSY/README
index 4e80c801fc00..7d462ea3f37a 100644
--- a/academic/EMBASSY/README
+++ b/academic/EMBASSY/README
@@ -1,9 +1,10 @@
-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 
+EMBASSY 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
+EMBASSY includes the following: CBSTOOLS, CLUSTALOMEGA, DOMAINATRIX,
+DOMALIGN, DOMSEARCH, DOMSEARCH, EMNU, ESIM4, HMMER, IPRSCAN, MEME,
+MSE, MYEMBOSS, MYEMBOSSDEMO, PHYLIPNEW, SIGNATURE, STRUCTURE, TOPO and
+VIENNA. For a more detailed description check the CONTENTS file.
diff --git a/academic/EMBASSY/slack-desc b/academic/EMBASSY/slack-desc
index 329780b6a13e..407970d31979 100644
--- a/academic/EMBASSY/slack-desc
+++ b/academic/EMBASSY/slack-desc
@@ -12,8 +12,8 @@ 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: Home: http://emboss.sourceforge.net/embassy/
 EMBASSY:
 EMBASSY:
 EMBASSY:
 EMBASSY:
-EMBASSY: Home: http://emboss.sourceforge.net/embassy/