From 24b14de22b60a7c5a1e4ee5fb4db9bc1d2b0b0e5 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 9 Sep 2022 02:53:27 +0100 Subject: academic/bpp1.9-utils: Added (Bio++ 1.9 Utils Library) Signed-off-by: Dave Woodfall --- academic/bpp1.9-utils/README | 10 +++ academic/bpp1.9-utils/bpp1.9-utils.SlackBuild | 120 ++++++++++++++++++++++++++ academic/bpp1.9-utils/bpp1.9-utils.info | 10 +++ academic/bpp1.9-utils/slack-desc | 19 ++++ 4 files changed, 159 insertions(+) create mode 100644 academic/bpp1.9-utils/README create mode 100644 academic/bpp1.9-utils/bpp1.9-utils.SlackBuild create mode 100644 academic/bpp1.9-utils/bpp1.9-utils.info create mode 100644 academic/bpp1.9-utils/slack-desc diff --git a/academic/bpp1.9-utils/README b/academic/bpp1.9-utils/README new file mode 100644 index 0000000000..5ee42d9632 --- /dev/null +++ b/academic/bpp1.9-utils/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) Utils 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-utils/bpp1.9-utils.SlackBuild b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild new file mode 100644 index 0000000000..6840376b84 --- /dev/null +++ b/academic/bpp1.9-utils/bpp1.9-utils.SlackBuild @@ -0,0 +1,120 @@ +#!/bin/bash + +# Slackware build script for bpp1.9-utils + +# 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-utils +SRCNAM=bpp-utils +VERSION=${VERSION:-1.5.0} +BUILD=${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 [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay! +LIBDIRPATH="-Wl,-rpath,/usr/lib${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 {} \; + +# This is needed on newer systems (-current) +#sed -i "s:file;:file.good();:g" Utils/FileTools.cpp + +# Use custom install place, so libs can coexist with latest Bio++ +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Utils.spec + +source /etc/profile.d/gcc5.sh + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + +# More about word boundary and sed: +# https://linuxize.com/post/how-to-use-sed-to-find-and-replace-string-in-files/ +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Utils/cmake_install.cmake +sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Utils/cmake_install.cmake + + make + make DESTDIR=$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 +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-utils/bpp1.9-utils.info b/academic/bpp1.9-utils/bpp1.9-utils.info new file mode 100644 index 0000000000..8ee8062200 --- /dev/null +++ b/academic/bpp1.9-utils/bpp1.9-utils.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-utils" +VERSION="1.5.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://raw.githubusercontent.com/slackalaxy/sources/main/bpp-utils-1.5.0.tar.gz" +MD5SUM="4625b7f2146caa1815ed7dc433d5eb78" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="gcc5" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.copm" diff --git a/academic/bpp1.9-utils/slack-desc b/academic/bpp1.9-utils/slack-desc new file mode 100644 index 0000000000..be9d333c61 --- /dev/null +++ b/academic/bpp1.9-utils/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-utils: bpp1.9-utils (Bio++ 1.9 Utils Library) +bpp1.9-utils: +bpp1.9-utils: Contains the Bio++ 1.9 Utils Library. +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: +bpp1.9-utils: -- cgit v1.2.3