academic/PhyML: Updated for version 20110526.

Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>

academic/PhyML/PhyML.SlackBuild

@@ -4,17 +4,19 @@
 # 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.
 
 PRGNAM=PhyML		
-VERSION=${VERSION:-3.0}
+VERSION=${VERSION:-20110526}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}	
 
 SRCNAM=$(echo $PRGNAM | tr A-Z a-z)
-SRCVER=2010023
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
@@ -48,9 +50,9 @@ set -e
 rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
-rm -rf $SRCNAM
-tar xvf $CWD/${SRCNAM}_$SRCVER.tar.gz
-cd $SRCNAM
+rm -rf $SRCNAM-$VERSION
+tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
+cd $SRCNAM-$VERSION
 chown -R root:root .
 find . \
  \( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
@@ -58,9 +60,6 @@ find . \
  \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
  -exec chmod 644 {} \;
 
-aclocal
-autoconf -f
-automake -f
 ./configure \
   --prefix=/usr \
   --libdir=/usr/lib${LIBDIRSUFFIX} \
@@ -70,11 +69,13 @@ automake -f
   --docdir=/usr/doc/$PRGNAM-$VERSION \
   --build=$ARCH-slackware-linux
 
-#Use our CFLAGS
-sed -i "/^AM_CFLAGS/s/=/+=/" src/Makefile
+# Use our CFLAGS
+sed -i "/^CFLAGS/s/=/+=/" src/Makefile
+sed -i "/^CFLAGS/s/=/+=/" Makefile
 
-AM_CFLAGS="$SLKCFLAGS" \
-  make
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+make
 make install DESTDIR=$PKG
 
 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
@@ -82,7 +83,7 @@ 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 INSTALL \
+  doc/phyml_manual.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

academic/PhyML/PhyML.info

@@ -1,8 +1,8 @@
 PRGNAM="PhyML"
-VERSION="3.0"
-HOMEPAGE="http://www.atgc-montpellier.fr/phyml/"
-DOWNLOAD="http://phyml.googlecode.com/files/phyml_2010023.tar.gz"
-MD5SUM="80a4e936a17b25ba0175e29d64285b05"
+VERSION="20110526"
+HOMEPAGE="http://code.google.com/p/phyml/"
+DOWNLOAD="http://phyml.googlecode.com/files/phyml-20110526.tar.gz"
+MD5SUM="04e707ee6e0bda6259e75ab82a87e818"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 MAINTAINER="Petar Petrov"

academic/PhyML/README

@@ -1,7 +1,13 @@
-PhyML is a phylogeny software based on the maximum-likelihood 
-principle. Early PhyML versions used a fast algorithm to perform 
-Nearest Neighbor Interchanges (NNIs), in order to improve a 
-reasonable starting tree topology. 
+PhyML is a software that estimates maximum likelihood phylogenies 
+from alignments of nucleotide or amino acid sequences. It provides a 
+wide range of options that were designed to facilitate standard 
+phylogenetic analyses. The main strengths of PhyML lies in the large 
+number of substitution models coupled to various options to search 
+the space of phylogenetic tree topologies, going from very fast and 
+efficient methods to slower but generally more accurate approaches. 
+It also implements two methods to evaluate branch supports in a sound 
+statistical framework (the non-parametric bootstrap and the 
+approximate likelihood ratio test).
 
 For details and citation
 New Algorithms and Methods to Estimate Maximum-Likelihood 

academic/PhyML/slack-desc

@@ -8,12 +8,12 @@
      |-----handy-ruler------------------------------------------------------|
 PhyML: PhyML (Phylogeny software)
 PhyML:
-PhyML: PhyML is a phylogeny software based on the maximum-likelihood
-PhyML: principle. Early PhyML versions used a fast algorithm to perform
-PhyML: Nearest Neighbor Interchanges (NNIs), in order to improve a
-PhyML: reasonable starting tree topology.
+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: phylogenetic analyses.
 PhyML:
 PhyML:
 PhyML:
 PhyML: References: /usr/doc/PhyML-$VERSION/References
-PhyML: Home: http://www.atgc-montpellier.fr/phyml/
+PhyML: Home: http://code.google.com/p/phyml/