diff options
Diffstat (limited to 'academic')
| -rw-r--r-- | academic/PhyML/PhyML.SlackBuild | 41 | ||||
| -rw-r--r-- | academic/PhyML/PhyML.info | 6 | ||||
| -rw-r--r-- | academic/PhyML/README | 11 | ||||
| -rw-r--r-- | academic/PhyML/slack-desc | 2 |
4 files changed, 34 insertions, 26 deletions
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild index d4b3d67cae7a..d82f9370f538 100644 --- a/academic/PhyML/PhyML.SlackBuild +++ b/academic/PhyML/PhyML.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for PhyML -# Copyright 2011-2016 Petar Petrov slackalaxy@gmail.com +# Copyright 2011-2017 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,13 +25,11 @@ # Thanks to Niels Horn for some handy modifications and corrections. PRGNAM=PhyML -VERSION=${VERSION:-3.2.20160530} +SRCNAM=$(echo $PRGNAM | tr A-Z a-z) +VERSION=${VERSION:-3.3.20170530} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} -SRCNAM=$(echo $PRGNAM | tr A-Z a-z) -SRCVER=3.2.20160530 - if [ -z "$ARCH" ]; then case "$( uname -m )" in i?86) ARCH=i586 ;; @@ -64,15 +62,9 @@ set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $SRCNAM-$SRCVER - -if [ -e $CWD/v${SRCVER}.tar.gz ]; then - tar xvf $CWD/v${SRCVER}.tar.gz -else - tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz -fi - -cd $SRCNAM-$SRCVER +rm -rf $SRCNAM-$VERSION +tar xvf $CWD/$SRCNAM-$VERSION.tar.gz +cd $SRCNAM-$VERSION chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -145,6 +137,27 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG +# This is PhyTime +./autogen.sh +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --enable-phytime \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +# Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" src/Makefile +sed -i "/^CFLAGS/s/=/+=/" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make +make install DESTDIR=$PKG + 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/PhyML/PhyML.info b/academic/PhyML/PhyML.info index 739d1befc05e..3a44d2b2b00b 100644 --- a/academic/PhyML/PhyML.info +++ b/academic/PhyML/PhyML.info @@ -1,8 +1,8 @@ PRGNAM="PhyML" -VERSION="3.2.20160530" +VERSION="3.3.20170530" HOMEPAGE="https://github.com/stephaneguindon/phyml/" -DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.2.20160530.tar.gz" -MD5SUM="7a4689e2de3ac9efd7586980b07331f0" +DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.3.20170530/phyml-3.3.20170530.tar.gz" +MD5SUM="8801c23dbdb295b6bbcd417f0010bb6a" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="openmpi" diff --git a/academic/PhyML/README b/academic/PhyML/README index fd66cda1231a..b6ce38f0bd4d 100644 --- a/academic/PhyML/README +++ b/academic/PhyML/README @@ -9,16 +9,11 @@ It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). -NOTE 1: This also builds Phyrex and the MPI (using multiple processors) -version of PhyML. The executable of the latter is called phyml-mpi and -requires openmpi. If you do not want them to be built in the package, +This also builds MPI (using multiple processors) version of PhyML, which +requires 'openmpi'. Other additional programs built by the script are +Phyrex and PhyTime. If you do not want them to be built in the package, check the SlackBuild script. -NOTE 2: PhyTime used to be part of the PhyML package. However, PhyTime -from the latest releases of PhyML does not build anymore. meanwhile, -PhyTime is available separately, which installs the latest version that -builds. - For details and citation New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S., diff --git a/academic/PhyML/slack-desc b/academic/PhyML/slack-desc index ae498120bb24..e03cd2812cb9 100644 --- a/academic/PhyML/slack-desc +++ b/academic/PhyML/slack-desc @@ -14,6 +14,6 @@ PhyML: wide range of options that were designed to facilitate standard PhyML: phylogenetic analyses. PhyML: PhyML: Home: http://code.google.com/p/phyml/ -PhyML: References: /usr/doc/PhyML-3.2.20160530/References +PhyML: References: /usr/doc/PhyML-3.3.20170530/References PhyML: PhyML: |