acacemic/EMBASSY: Updated for version 6.5.7.

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

1 files changed, 103 insertions, 203 deletions

diff --git a/academic/EMBASSY/EMBASSY.SlackBuild b/academic/EMBASSY/EMBASSY.SlackBuild
index 6a4d1b2794..eb67a7adcf 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