academic/seaview: Updated for version 4.3.2.

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

5 files changed, 47 insertions, 24 deletions

diff --git a/academic/seaview/README b/academic/seaview/README
index 8e1bd893b4b5..21de5ab1c563 100644
--- a/academic/seaview/README
+++ b/academic/seaview/README
@@ -9,14 +9,17 @@ sequence alignment and molecular phylogeny. Important features are:
    alignment, and also allows to use any external alignment algorithm 
    able to read and write FASTA-formatted files.
    
-3) SeaView computes phylogenetic trees by
+3) Seaview drives the Gblocks program to select blocks of 
+   evolutionarily conserved sites.
+   
+4) SeaView computes phylogenetic trees by
 	a) parsimony, using PHYLIP's dnapars/protpars algorithm,
 	b) distance, with NJ or BioNJ algorithms on a variety of 
 	   evolutionary distances,
 	c) maximum likelihood, driving program PhyML 3.0.
 	 
-4) SeaView draws phylogenetic trees on screen, PDF or PostScript files
-5) SeaView allows to download sequences from EMBL/GenBank/UniProt 
+5) SeaView draws phylogenetic trees on screen, PDF or PostScript files
+6) SeaView allows to download sequences from EMBL/GenBank/UniProt 
    using the Internet.
 
 For details and citation:
@@ -25,6 +28,5 @@ multiplatform graphical user interface for sequence alignment and
 phylogenetic tree building. Molecular Biology and Evolution 
 27(2):221-224. 
 
-Seaview requires fltk as a build depencency, but you need clustalw, 
-PhyML and muscle, which SeaView drives. All of these are available at 
-SlackBuilds.org. 
+This requires fltk as a build dependency, but you also need clustalw,
+Gblocks, PhyML, and muscle, all of which SeaView drives.
diff --git a/academic/seaview/seaview.SlackBuild b/academic/seaview/seaview.SlackBuild
index 6e8967e0da37..238764fd4303 100644
--- a/academic/seaview/seaview.SlackBuild
+++ b/academic/seaview/seaview.SlackBuild
@@ -1,17 +1,33 @@
 #!/bin/sh
 
 # Slackware build script for seaview
-# 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  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.
+
+# Thanks to Niels Horn for correcting the CFLAGS.
 
 PRGNAM=seaview			
-VERSION=${VERSION:-4.3.0}	
+VERSION=${VERSION:-4.3.2}	
 BUILD=${BUILD:-1}
-TAG=${TAG:-_SBo}		
+TAG=${TAG:-_SBo}
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
@@ -46,7 +62,7 @@ rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
 rm -rf $PRGNAM
-tar xvf $CWD/$PRGNAM.tar.gz
+tar xvf $CWD/${PRGNAM}_${VERSION}.tar.gz
 cd $PRGNAM
 chown -R root:root .
 find . \
@@ -55,15 +71,20 @@ find . \
  \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
  -exec chmod 644 {} \;
 
-#Use our CFLAGS
+# Use our CFLAGS
 sed -i "/^CFLAGS/s/=/+=/" Makefile
 
+# Point to the correct documentation path and phyml executable name
+sed -i "s:#HELPFILE:HELPFILE:" Makefile
+sed -i "s:/share/doc/seaview:/doc/$PRGNAM-$VERSION/:" Makefile
+sed -i "s:#PHYMLNAME:PHYMLNAME:" Makefile
+
 CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
   make
 
-install -D -m755 seaview $PKG/usr/bin/seaview
-install -D -m644 seaview.1 $PKG/usr/man/man1/seaview.1
+install -D -m755 seaview $PKG/usr/bin/$PRGNAM
+install -D -m644 seaview.1 $PKG/usr/man/man1/$PRGNAM.1
 
 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
   | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
diff --git a/academic/seaview/seaview.desktop b/academic/seaview/seaview.desktop
index be832dc37312..de14680455f8 100644
--- a/academic/seaview/seaview.desktop
+++ b/academic/seaview/seaview.desktop
@@ -1,7 +1,7 @@
 [Desktop Entry]
 Categories=Education;
 Exec=seaview
-Icon=seaview.xpm
-Name=Seaview
+Icon=seaview
+Name=SeaView
 StartupNotify=false
 Type=Application
diff --git a/academic/seaview/seaview.info b/academic/seaview/seaview.info
index 8603a2ca3949..299da38f30ed 100644
--- a/academic/seaview/seaview.info
+++ b/academic/seaview/seaview.info
@@ -1,8 +1,8 @@
 PRGNAM="seaview"
-VERSION="4.3.0"
+VERSION="4.3.2"
 HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
-DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview.tar.gz"
-MD5SUM="dc56d18e63c4c9110d9cf6198c86bd34"
+DOWNLOAD="http://pbil.univ-lyon1.fr/software/seaview_data/seaview_4.3.2.tar.gz"
+MD5SUM="d8b87a19d9cc4ee89478d647a6454fb2"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 MAINTAINER="Petar Petrov"
diff --git a/academic/seaview/slack-desc b/academic/seaview/slack-desc
index 901dc2c0f556..774e04f9ce24 100644
--- a/academic/seaview/slack-desc
+++ b/academic/seaview/slack-desc
@@ -11,9 +11,9 @@ seaview:
 seaview: SeaView is a multiplatform, graphical user interface for multiple
 seaview: sequence alignment and molecular phylogeny.
 seaview:
+seaview: References: /usr/doc/seaview-$VERSION/References
+seaview: Home: http://pbil.univ-lyon1.fr/software/seaview.html
 seaview:
 seaview:
 seaview:
 seaview:
-seaview: References: /usr/doc/seaview-$VERSION/References
-seaview: Home: http://pbil.univ-lyon1.fr/software/seaview.html