From 0fe8cde2ade7f19eebd9d9b3a9551955128196b7 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 9 Oct 2020 02:53:15 +0100 Subject: academic/bpp1.9-numcalc: Added (Bio++ 1.9 NumCalc Library) Signed-off-by: Dave Woodfall Signed-off-by: Willy Sudiarto Raharjo --- academic/bpp1.9-numcalc/README | 10 ++ academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild | 109 ++++++++++++++++++++++ academic/bpp1.9-numcalc/bpp1.9-numcalc.info | 10 ++ academic/bpp1.9-numcalc/slack-desc | 19 ++++ 4 files changed, 148 insertions(+) create mode 100644 academic/bpp1.9-numcalc/README create mode 100644 academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild create mode 100644 academic/bpp1.9-numcalc/bpp1.9-numcalc.info create mode 100644 academic/bpp1.9-numcalc/slack-desc diff --git a/academic/bpp1.9-numcalc/README b/academic/bpp1.9-numcalc/README new file mode 100644 index 0000000000..a514a0450e --- /dev/null +++ b/academic/bpp1.9-numcalc/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) NumCalc 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-numcalc/bpp1.9-numcalc.SlackBuild b/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild new file mode 100644 index 0000000000..4c23467bad --- /dev/null +++ b/academic/bpp1.9-numcalc/bpp1.9-numcalc.SlackBuild @@ -0,0 +1,109 @@ +#!/bin/sh + +# Slackware build script for bpp1.9-utils + +# Copyright 2020 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. + +PRGNAM=bpp1.9-numcalc +SRCNAM=bpp-numcalc +VERSION=${VERSION:-1.8.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +CWD=$(pwd) +TMP=${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 Urachlay! +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 {} \; + +# Use custom install place, so libs can coexist with latest bpp +export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH" +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" NumCalc.spec + +mkdir -p build +cd build + cmake \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + +sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" NumCalc/cmake_install.cmake +sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" NumCalc/cmake_install.cmake + + make + make DESTDIR=$PKG install +cd .. + +rm -f $PKG/usr/lib$LIBDIRSUFFIX/Bpp1.9/libbpp-numcalc.a + +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 INSTALL \ + $PKG/usr/doc/$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:-tgz} diff --git a/academic/bpp1.9-numcalc/bpp1.9-numcalc.info b/academic/bpp1.9-numcalc/bpp1.9-numcalc.info new file mode 100644 index 0000000000..0a1c619ed1 --- /dev/null +++ b/academic/bpp1.9-numcalc/bpp1.9-numcalc.info @@ -0,0 +1,10 @@ +PRGNAM="bpp1.9-numcalc" +VERSION="1.8.0" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="http://biopp.univ-montp2.fr/repos/sources/bpp-numcalc-1.8.0.tar.gz" +MD5SUM="0d6d51aaefcb4f89816704feae010bc9" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp1.9-utils" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp1.9-numcalc/slack-desc b/academic/bpp1.9-numcalc/slack-desc new file mode 100644 index 0000000000..0b1db4fe56 --- /dev/null +++ b/academic/bpp1.9-numcalc/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-numcalc: bpp1.9-numcalc (Bio++ 1.9 NumCalc Library) +bpp1.9-numcalc: +bpp1.9-numcalc: Contains the Bio++ 1.9 NumCalc Library. +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: +bpp1.9-numcalc: -- cgit v1.2.3