academic/PhyML: Updated for version 20110919.

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

4 files changed, 32 insertions, 21 deletions

diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild
index 05fb80d8cc..08ee51b623 100644
--- a/academic/PhyML/PhyML.SlackBuild
+++ b/academic/PhyML/PhyML.SlackBuild
@@ -1,18 +1,31 @@
 #!/bin/sh
 
 # Slackware build script for PhyML
-# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and 
-# hereby submitted to the public domain
 
-# Thanks to Niels Horn for the handy modifications and
-# corrections!
-
-# 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 some handy modifications and corrections.
 
 PRGNAM=PhyML		
-VERSION=${VERSION:-20110526}
+VERSION=${VERSION:-20110919}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}	
 
@@ -83,7 +96,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr
 
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  doc/phyml_manual.pdf AUTHORS ChangeLog COPYING INSTALL README \
+  doc/$SRCNAM-manual-$VERSION.pdf AUTHORS ChangeLog COPYING INSTALL README \
   $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info
index 9eb0f43c06..334dc43132 100644
--- a/academic/PhyML/PhyML.info
+++ b/academic/PhyML/PhyML.info
@@ -1,10 +1,10 @@
 PRGNAM="PhyML"
-VERSION="20110526"
+VERSION="20110919"
 HOMEPAGE="http://code.google.com/p/phyml/"
-DOWNLOAD="http://phyml.googlecode.com/files/phyml-20110526.tar.gz"
-MD5SUM="04e707ee6e0bda6259e75ab82a87e818"
+DOWNLOAD="http://phyml.googlecode.com/files/phyml-20110919.tar.gz"
+MD5SUM="d95c73c5c03d082db21564a54978f281"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 MAINTAINER="Petar Petrov"
 EMAIL="ppetrov@paju.oulu.fi"
-APPROVED="Niels Horn"
+APPROVED="rworkman"
diff --git a/academic/PhyML/References b/academic/PhyML/References
index 0d69b95fe4..17fd35add2 100644
--- a/academic/PhyML/References
+++ b/academic/PhyML/References
@@ -1,5 +1,3 @@
-References
-
 New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies:
 Assessing the Performance of PhyML 3.0. Guindon S., Dufayard J.F.,
 Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology,
diff --git a/academic/PhyML/slack-desc b/academic/PhyML/slack-desc
index a4ddd88a6a..be2d634abf 100644
--- a/academic/PhyML/slack-desc
+++ b/academic/PhyML/slack-desc
@@ -6,14 +6,14 @@
 # customary to leave one space after the ':'.
 
      |-----handy-ruler------------------------------------------------------|
-PhyML: PhyML (Phylogeny software)
+PhyML: PhyML (Phylogenetic estimation using Maximum Likelihood)
 PhyML:
 PhyML: PhyML is a software that estimates maximum likelihood phylogenies
-PhyML: from alignments of nucleotide or amino acid sequences. It provides a
-PhyML: wide range of options that were designed to facilitate standard
+PhyML: from alignments of nucleotide or amino acid sequences. It provides
+PhyML: a wide range of options that were designed to facilitate standard
 PhyML: phylogenetic analyses.
 PhyML:
-PhyML:
-PhyML:
 PhyML: References: /usr/doc/PhyML-$VERSION/References
 PhyML: Home: http://code.google.com/p/phyml/
+PhyML:
+PhyML: