academic/EMBOSS: Updated for version 6.5.7.

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

academic/EMBOSS/EMBOSS.SlackBuild

@@ -1,17 +1,31 @@
 #!/bin/sh
 
 # Slackware build script for EMBOSS
-# 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.
+# 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=EMBOSS			
-VERSION=${VERSION:-6.4.0}
-BUILD=${BUILD:-3}
-TAG=${TAG:-_SBo}	
+PRGNAM=EMBOSS
+VERSION=${VERSION:-6.5.7}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
@@ -49,9 +63,6 @@ rm -rf $PRGNAM-$VERSION
 tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
 cd $PRGNAM-$VERSION
 
-# Apply EMBOSS bug-fix set 1-24. Thanks to Alan at ajb@ebi.ac.uk!
-patch -p1 < $CWD/patch-1-24
-
 chown -R root:root .
 find . \
  \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
@@ -59,6 +70,9 @@ find . \
  \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
  -exec chmod 644 {} \;
 
+# We do not need to check for EMBOSS updates
+sed -i "/embossupdate/d" Makefile.am Makefile.in
+
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
@@ -67,6 +81,7 @@ CXXFLAGS="$SLKCFLAGS" \
   --with-x \
   --sysconfdir=/etc \
   --localstatedir=/var \
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
   --build=$ARCH-slackware-linux
 
 make
@@ -77,14 +92,14 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  AUTHORS ChangeLog COPYING FAQ INSTALL NEWS README THANKS \
+  AUTHORS ChangeLog COPYING FAQ INSTALL LICENSE NEWS README THANKS \
   $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
 
 mkdir -p $PKG/usr/share/{applications,pixmaps}
-cp $CWD/emboss.desktop $PKG/usr/share/applications
-cp $CWD/emboss.png $PKG/usr/share/pixmaps
+cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications
+cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps
 
 mkdir -p $PKG/install
 cat $CWD/slack-desc > $PKG/install/slack-desc

academic/EMBOSS/EMBOSS.desktop

@@ -1,8 +1,9 @@
 [Desktop Entry]
 Categories=Education;
 Comment=Bioinformatics suite
-Exec=runJemboss.csh
-Icon=emboss.png
+Exec=runJemboss.sh
+Icon=EMBOSS.png
 Name=EMBOSS
 StartupNotify=false
 Type=Application
+GenericName=

academic/EMBOSS/EMBOSS.info

@@ -1,8 +1,8 @@
 PRGNAM="EMBOSS"
-VERSION="6.4.0"
+VERSION="6.5.7"
 HOMEPAGE="http://emboss.sourceforge.net/"
-DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/old/6.4.0/EMBOSS-6.4.0.tar.gz"
-MD5SUM="54993a22064222b01bd4fc8086f7684d"
+DOWNLOAD="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.5.7.tar.gz"
+MD5SUM="6a2cb3f93d5e9415c74ab0f6b1ede5f0"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES="jdk"

academic/EMBOSS/README

@@ -1,19 +1,32 @@
-EMBOSS is "The European Molecular Biology Open Software Suite". 
+EMBOSS is "The European Molecular Biology Open Software Suite".
 
-EMBOSS is a free Open Source software analysis package specially 
-developed for the needs of the molecular biology (e.g. EMBnet) user 
-community. The software automatically copes with data in a variety of 
-formats and even allows transparent retrieval of sequence data from 
-the web. Also, as extensive libraries are provided with the package, 
-it is a platform to allow other scientists to develop and release 
+EMBOSS is a free Open Source software analysis package specially
+developed for the needs of the molecular biology (e.g. EMBnet) user
+community. The software automatically copes with data in a variety of
+formats and even allows transparent retrieval of sequence data from
+the web. Also, as extensive libraries are provided with the package,
+it is a platform to allow other scientists to develop and release
 software in true open source spirit. EMBOSS also integrates a range of
-currently available packages and tools for sequence analysis into a 
-seamless whole. EMBOSS breaks the historical trend towards commercial 
+currently available packages and tools for sequence analysis into a
+seamless whole. EMBOSS breaks the historical trend towards commercial
 software packages.
 
-For details and citation:
-EMBOSS: The European Molecular Biology Open Software Suite (2000) 
-Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276-277 
+Within EMBOSS you will find around hundreds of programs (applications)
+covering areas such as:
 
-If you want to use eprimer3 and multiple sequence alignment programs 
-like emma, you should install primer3 and clustalw.
+- Sequence alignment
+- Rapid database searching with sequence patterns
+- Protein motif identification, including domain analysis
+- Nucleotide sequence pattern analysis -- for example to identify CpG
+  islands or repeats
+- Codon usage analysis for small genomes
+- Rapid identification of sequence patterns in large scale sequence
+  sets
+- Presentation tools for publication
+
+Optional, run-time dependencies are clustalw and primer3 -- needed if
+you want to use the wrappers emma and eprimer32.
+
+For details and citation:
+EMBOSS: The European Molecular Biology Open Software Suite (2000)
+Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276-277

academic/EMBOSS/References

@@ -1,4 +1,2 @@
-References
-
 EMBOSS: The European Molecular Biology Open Software Suite (2000)
 Rice,P. Longden,I. and Bleasby,A. Trends in Genetics 16, (6) pp276--277

academic/EMBOSS/slack-desc

@@ -12,8 +12,8 @@ EMBOSS: EMBOSS is a free Open Source software analysis package specially
 EMBOSS: developed for the needs of the molecular biology (e.g. EMBnet)
 EMBOSS: user community.
 EMBOSS:
-EMBOSS:
-EMBOSS:
-EMBOSS:
 EMBOSS: References: /usr/doc/EMBOSS-$VERSION/References
+EMBOSS: Details: /usr/share/EMBOSS/doc
 EMBOSS: Home: http://emboss.sourceforge.net/
+EMBOSS:
+EMBOSS: