From 1f0ff62f35d302c3ca0868682d5475a5b5a80f55 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 9 Sep 2022 03:07:45 +0100 Subject: academic/bpp1.9-phyl: Added (Bio++ 1.9 Phyl Library) Signed-off-by: Dave Woodfall --- academic/bpp1.9-phyl/README | 10 ++ academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild | 119 ++++++++++++++++++++++ academic/bpp1.9-phyl/bpp1.9-phyl.info | 10 ++ academic/bpp1.9-phyl/caps_TreeTemplateTools.patch | 39 +++++++ academic/bpp1.9-phyl/slack-desc | 19 ++++ 5 files changed, 197 insertions(+) create mode 100644 academic/bpp1.9-phyl/README create mode 100644 academic/bpp1.9-phyl/bpp1.9-phyl.SlackBuild create mode 100644 academic/bpp1.9-phyl/bpp1.9-phyl.info create mode 100644 academic/bpp1.9-phyl/caps_TreeTemplateTools.patch create mode 100644 academic/bpp1.9-phyl/slack-desc diff --git a/academic/bpp1.9-phyl/README b/academic/bpp1.9-phyl/README new file mode 100644 index 0000000000..292485c428 --- /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 0000000000..fa951d6f2e --- /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 0000000000..ae873c0a59 --- /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 0000000000..b4f79029de --- /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& 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 0000000000..05245c02f1 --- /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: -- cgit v1.2.3