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-rw-r--r--academic/PhyML/PhyML.SlackBuild27
-rw-r--r--academic/PhyML/PhyML.info8
-rw-r--r--academic/PhyML/README14
-rw-r--r--academic/PhyML/slack-desc10
4 files changed, 33 insertions, 26 deletions
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild
index 5fb6ce9fcf..05fb80d8cc 100644
--- a/academic/PhyML/PhyML.SlackBuild
+++ b/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
diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info
index 8008d1b6ba..9eb0f43c06 100644
--- a/academic/PhyML/PhyML.info
+++ b/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"
diff --git a/academic/PhyML/README b/academic/PhyML/README
index f86217a2ad..59a8afefb5 100644
--- a/academic/PhyML/README
+++ b/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
diff --git a/academic/PhyML/slack-desc b/academic/PhyML/slack-desc
index 00859ef7ab..a4ddd88a6a 100644
--- a/academic/PhyML/slack-desc
+++ b/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/