From 76a9808c95a1088f2ceda0ae0ad48c3dd3bbb17f Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Tue, 2 May 2017 22:16:10 +0700 Subject: academic/bpp-popgen: Added (Bio++ Population Genetics Library). Signed-off-by: Willy Sudiarto Raharjo --- academic/bpp-popgen/README | 8 +++ academic/bpp-popgen/bpp-popgen.SlackBuild | 98 +++++++++++++++++++++++++++++++ academic/bpp-popgen/bpp-popgen.info | 10 ++++ academic/bpp-popgen/slack-desc | 19 ++++++ 4 files changed, 135 insertions(+) create mode 100644 academic/bpp-popgen/README create mode 100644 academic/bpp-popgen/bpp-popgen.SlackBuild create mode 100644 academic/bpp-popgen/bpp-popgen.info create mode 100644 academic/bpp-popgen/slack-desc (limited to 'academic/bpp-popgen') diff --git a/academic/bpp-popgen/README b/academic/bpp-popgen/README new file mode 100644 index 0000000000..0772158a82 --- /dev/null +++ b/academic/bpp-popgen/README @@ -0,0 +1,8 @@ +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++ Population Genetics Library. diff --git a/academic/bpp-popgen/bpp-popgen.SlackBuild b/academic/bpp-popgen/bpp-popgen.SlackBuild new file mode 100644 index 0000000000..9a3c94f92b --- /dev/null +++ b/academic/bpp-popgen/bpp-popgen.SlackBuild @@ -0,0 +1,98 @@ +#!/bin/sh + +# Slackware build script for bpp-phyl + +# Copyright 2017 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=bpp-popgen +VERSION=${VERSION:-git_d40aa82} +COMMIT=d40aa82d365cd98a249e98ca6f6a4610db7ad03e +BUILD=${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 + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$COMMIT +tar xvf $CWD/$PRGNAM-$COMMIT.tar.gz +cd $PRGNAM-$COMMIT +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 {} \; + +sed -i "s|cmake-package-location lib/cmake|cmake-package-location lib${LIBDIRSUFFIX}/cmake|" CMakeLists.txt + +mkdir -p build +cd build + cmake \ + -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DLIB_SUFFIX=${LIBDIRSUFFIX} \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$PKG +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.txt ChangeLog COPYING.txt INSTALL.txt $PKG/usr/doc/$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/bpp-popgen/bpp-popgen.info b/academic/bpp-popgen/bpp-popgen.info new file mode 100644 index 0000000000..980586c95a --- /dev/null +++ b/academic/bpp-popgen/bpp-popgen.info @@ -0,0 +1,10 @@ +PRGNAM="bpp-popgen" +VERSION="git_d40aa82" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://github.com/BioPP/bpp-popgen/archive/d40aa82/bpp-popgen-d40aa82d365cd98a249e98ca6f6a4610db7ad03e.tar.gz" +MD5SUM="0665c910437f571526636f7a083af917" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp-seq" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp-popgen/slack-desc b/academic/bpp-popgen/slack-desc new file mode 100644 index 0000000000..f59a1bdccd --- /dev/null +++ b/academic/bpp-popgen/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------------------------------------------------------| +bpp-popgen: bpp-popgen (Bio++ Population Genetics Library) +bpp-popgen: +bpp-popgen: Contains the Bio++ Population Genetics Library. +bpp-popgen: +bpp-popgen: Git: https://github.com/BioPP/bpp-popgen +bpp-popgen: +bpp-popgen: +bpp-popgen: +bpp-popgen: +bpp-popgen: +bpp-popgen: -- cgit v1.2.3