academic/bpp1.9-phyl: Added (Bio++ 1.9 Phyl Library)

Signed-off-by: Dave Woodfall <dave@slackbuilds.org>

5 files changed, 197 insertions, 0 deletions

diff --git a/academic/bpp1.9-phyl/README b/academic/bpp1.9-phyl/README
new file mode 100644
index 0000000000000..292485c428638
--- /dev/null
+++ b/academic/bpp1.9-phyl/README
@@ -0,0 +1,10 @@
+Bio++ is a set of C++ libraries for Bioinformatics, including sequence
+analysis, phylogenetics, molecular evolution and population genetics.
+Bio++ is Object Oriented and is designed to be both easy to use and
+computer efficient. Bio++ intends to help programmers to write
+computer expensive programs, by providing them a set of re-usable
+tools.
+
+This contains the Bio++ 1.9 (April 2010) Phyl Library. It can be
+installed along the current Bio++ suite libraries, however they better
+not be present at compile time.
diff --git a/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild
new file mode 100644
index 0000000000000..fa951d6f2e6a2
--- /dev/null
+++ b/academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild
@@ -0,0 +1,119 @@
+#!/bin/bash
+
+# Slackware build script for bpp1.9-phyl
+
+# Copyright 2020-2022 Petar Petrov slackalaxy@gmail.com
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+cd $(dirname $0) ; CWD=$(pwd)
+
+PRGNAM=bpp1.9-phyl
+SRCNAM=bpp-phyl
+VERSION=${VERSION:-1.9.0}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+PKGTYPE=${PKGTYPE:-tgz}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
+  echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
+  exit 0
+fi
+
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+  LIBDIRSUFFIX=""
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+  LIBDIRSUFFIX="64"
+else
+  SLKCFLAGS="-O2"
+  LIBDIRSUFFIX=""
+fi
+
+LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9"
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $SRCNAM-$VERSION
+tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
+cd $SRCNAM-$VERSION
+chown -R root:root .
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+# CAPS wants TreeTemplateTools to be modified a bit...
+patch -p1 -i $CWD/caps_TreeTemplateTools.patch
+
+# Use custom install place, so libs can coexist with latest bpp
+export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH"
+sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl.spec
+
+source /etc/profile.d/gcc5.sh
+
+mkdir -p build
+cd build
+  cmake \
+    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DCMAKE_BUILD_TYPE=Release ..
+
+  sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Phyl/cmake_install.cmake
+  sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Phyl/cmake_install.cmake
+
+  make
+  make DESTDIR=$PKG install
+cd ..
+
+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
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+chmod 0644 AUTHORS ChangeLog COPYING
+cp -a \
+  AUTHORS ChangeLog COPYING \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
diff --git a/academic/bpp1.9-phyl/bpp1.9-phyl.info b/academic/bpp1.9-phyl/bpp1.9-phyl.info
new file mode 100644
index 0000000000000..ae873c0a59905
--- /dev/null
+++ b/academic/bpp1.9-phyl/bpp1.9-phyl.info
@@ -0,0 +1,10 @@
+PRGNAM="bpp1.9-phyl"
+VERSION="1.9.0"
+HOMEPAGE="http://biopp.univ-montp2.fr/"
+DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-phyl-1.9.0.tar.gz"
+MD5SUM="1b100b688faca52419e9f782798b8add"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES="bpp1.9-seq"
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch b/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch
new file mode 100644
index 0000000000000..b4f79029de515
--- /dev/null
+++ b/academic/bpp1.9-phyl/caps_TreeTemplateTools.patch
@@ -0,0 +1,39 @@
+diff -pruN orig/Phyl/TreeTemplateTools.h new/Phyl/TreeTemplateTools.h
+--- orig/Phyl/TreeTemplateTools.h	2010-04-01 16:37:04.000000000 +0300
++++ new/Phyl/TreeTemplateTools.h	2017-02-03 14:33:11.000000000 +0200
+@@ -191,7 +191,7 @@ class TreeTemplateTools
+     static void dropLeaf(TreeTemplate<N>& tree, const std::string& leafName) throw (NodeNotFoundException, Exception)
+     {
+       N* leaf = tree.getNode(leafName);
+-      if (!leaf->hasfather())
++      if (!leaf->hasFather())
+         throw Exception("TreeTemplateTools::dropLeaf(). Leaf is the only node in the tree, can't remove it.");
+       N* parent = leaf->getFather();
+       if (parent->getNumberOfSons() > 2)
+@@ -203,7 +203,7 @@ class TreeTemplateTools
+       else if (parent->getNumberOfSons() == 2)
+       {
+         //We have to delete the parent node as well:
+-        N* brother = parent->getson(0);
++        N* brother = parent->getSon(0);
+         if (brother == leaf) brother = parent->getSon(1);
+         if (!parent->hasFather())
+         {
+@@ -212,7 +212,7 @@ class TreeTemplateTools
+           {
+             brother->setDistanceToFather(brother->getDistanceToFather() + leaf->getDistanceToFather());
+           }
+-          tree->setRootNode(brother);
++          tree.setRootNode(brother);
+           delete parent;
+           delete leaf;
+         }
+@@ -223,7 +223,7 @@ class TreeTemplateTools
+           {
+             brother->setDistanceToFather(brother->getDistanceToFather() + parent->getDistanceToFather());
+           }
+-          unsigned int pos = gParent->getsonPosition(parent);
++          unsigned int pos = gParent->getSonPosition(parent);
+           gParent->setSon(pos, brother);
+           delete parent;
+           delete leaf;
diff --git a/academic/bpp1.9-phyl/slack-desc b/academic/bpp1.9-phyl/slack-desc
new file mode 100644
index 0000000000000..05245c02f105d
--- /dev/null
+++ b/academic/bpp1.9-phyl/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+           |-----handy-ruler------------------------------------------------------|
+bpp1.9-phyl: bpp1.9-phyl (Bio++ 1.9 Phyl Library)
+bpp1.9-phyl:
+bpp1.9-phyl: Contains the Bio++ 1.9 Phyl Library.
+bpp1.9-phyl:
+bpp1.9-phyl:
+bpp1.9-phyl:
+bpp1.9-phyl:
+bpp1.9-phyl:
+bpp1.9-phyl:
+bpp1.9-phyl:
+bpp1.9-phyl: