academic/PhyML: Updated for version 3.2.20160530.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

academic/PhyML/PhyML.SlackBuild

@@ -25,16 +25,16 @@
 # Thanks to Niels Horn for some handy modifications and corrections.
 
 PRGNAM=PhyML
-VERSION=${VERSION:-20131112}
+VERSION=${VERSION:-3.2.20160530}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
 SRCNAM=$(echo $PRGNAM | tr A-Z a-z)
-SRCVER=20120412
+SRCVER=3.2.20160530
 
 if [ -z "$ARCH" ]; then
   case "$( uname -m )" in
-    i?86) ARCH=i486 ;;
+    i?86) ARCH=i586 ;;
     arm*) ARCH=arm ;;
        *) ARCH=$( uname -m ) ;;
   esac
@@ -45,8 +45,8 @@ TMP=${TMP:-/tmp/SBo}
 PKG=$TMP/package-$PRGNAM
 OUTPUT=${OUTPUT:-/tmp}
 
-if [ "$ARCH" = "i486" ]; then
-  SLKCFLAGS="-O2 -march=i486 -mtune=i686"
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
   LIBDIRSUFFIX=""
 elif [ "$ARCH" = "i686" ]; then
   SLKCFLAGS="-O2 -march=i686 -mtune=i686"
@@ -65,7 +65,13 @@ rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
 rm -rf $SRCNAM-$SRCVER
-tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz
+
+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
 chown -R root:root .
 find -L . \
@@ -74,18 +80,16 @@ find -L . \
  \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-# Apply version patch
-cd src
-  patch -i $CWD/$VERSION.patch
-cd ..
-
-# This is PhyML
+# This is PhyML, the main component of the package. If this is all you want, you
+# can comment out the sections that build PhyML MPI and Phyrex below.
+./autogen.sh
 ./configure \
   --prefix=/usr \
   --libdir=/usr/lib${LIBDIRSUFFIX} \
   --sysconfdir=/etc \
   --localstatedir=/var \
   --mandir=/usr/man \
+  --enable-phyml \
   --docdir=/usr/doc/$PRGNAM-$VERSION \
   --build=$ARCH-slackware-linux
 
@@ -98,14 +102,37 @@ CXXFLAGS="$SLKCFLAGS" \
 make
 make install DESTDIR=$PKG
 
-# And this is PhyTime
+# This is PhyML MPI. If you do not want it, comment the lines below. Then you do
+# not need to install openmpi.
+./autogen.sh
 ./configure \
   --prefix=/usr \
   --libdir=/usr/lib${LIBDIRSUFFIX} \
   --sysconfdir=/etc \
   --localstatedir=/var \
-  --enable-phytime \
   --mandir=/usr/man \
+  --enable-mpi \
+  --docdir=/usr/doc/$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=$PKG
+
+# This is Phyrex
+./autogen.sh
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --mandir=/usr/man \
+  --enable-phyrex \
   --docdir=/usr/doc/$PRGNAM-$VERSION \
   --build=$ARCH-slackware-linux
 
@@ -121,9 +148,15 @@ 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
 
+# Include some examples
+mkdir -p $PKG/usr/share/$PRGNAM
+cp -a \
+  examples/{lg4x,phyrex_input_files,nexus_example.nxs,nucleic,proteic} \
+  $PKG/usr/share/$PRGNAM
+
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  doc/$SRCNAM-manual-20120306.pdf AUTHORS ChangeLog COPYING INSTALL README \
+  doc/$SRCNAM-manual.pdf AUTHORS ChangeLog COPYING LICENSE 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

@@ -1,10 +1,10 @@
 PRGNAM="PhyML"
-VERSION="20131112"
-HOMEPAGE="http://code.google.com/p/phyml/"
-DOWNLOAD="http://phyml.googlecode.com/files/phyml-20120412.tar.gz"
-MD5SUM="d2207a3d6caf633c43239a01ce70f244"
+VERSION="3.2.20160530"
+HOMEPAGE="https://github.com/stephaneguindon/phyml/"
+DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.2.20160530.tar.gz"
+MD5SUM="7a4689e2de3ac9efd7586980b07331f0"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES=""
+REQUIRES="openmpi"
 MAINTAINER="Petar Petrov"
 EMAIL="slackalaxy@gmail.com"

academic/PhyML/README

@@ -9,7 +9,15 @@ It also implements two methods to evaluate branch supports in a sound
 statistical framework (the non-parametric bootstrap and the
 approximate likelihood ratio test).
 
-The script also builds the additional program PhyTime.
+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,
+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

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-20131112/References
+PhyML: References: /usr/doc/PhyML-3.2.20160530/References
 PhyML:
 PhyML: