diff options
| -rw-r--r-- | academic/PhyML/PhyML.SlackBuild | 27 | ||||
| -rw-r--r-- | academic/PhyML/PhyML.info | 8 | ||||
| -rw-r--r-- | academic/PhyML/README | 14 | ||||
| -rw-r--r-- | academic/PhyML/slack-desc | 10 |
4 files changed, 33 insertions, 26 deletions
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild index 5fb6ce9fcfbff..05fb80d8cc26c 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 8008d1b6ba376..9eb0f43c064fb 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 f86217a2ad53e..59a8afefb5df7 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 00859ef7ab834..a4ddd88a6a629 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/ |