From 80d8f04b6bb875904010ffe97cd1014042c79059 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Tue, 2 May 2017 22:12:06 +0700 Subject: academic/bpp-phyl-omics: Added (Bio++ Phylogenetic Omics Library). Signed-off-by: Willy Sudiarto Raharjo --- academic/bpp-phyl-omics/README | 8 ++ academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild | 98 +++++++++++++++++++++++ academic/bpp-phyl-omics/bpp-phyl-omics.info | 10 +++ academic/bpp-phyl-omics/slack-desc | 19 +++++ 4 files changed, 135 insertions(+) create mode 100644 academic/bpp-phyl-omics/README create mode 100644 academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild create mode 100644 academic/bpp-phyl-omics/bpp-phyl-omics.info create mode 100644 academic/bpp-phyl-omics/slack-desc (limited to 'academic/bpp-phyl-omics') diff --git a/academic/bpp-phyl-omics/README b/academic/bpp-phyl-omics/README new file mode 100644 index 0000000000..c5ebc164c7 --- /dev/null +++ b/academic/bpp-phyl-omics/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++ Phylogenetic Omics Library. diff --git a/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild b/academic/bpp-phyl-omics/bpp-phyl-omics.SlackBuild new file mode 100644 index 0000000000..ead022b0ac --- /dev/null +++ b/academic/bpp-phyl-omics/bpp-phyl-omics.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-phyl-omics +VERSION=${VERSION:-git_2a61eee} +COMMIT=2a61eeee355cb9d7c5e774215307cd1876c8fbda +BUILD=${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-phyl-omics/bpp-phyl-omics.info b/academic/bpp-phyl-omics/bpp-phyl-omics.info new file mode 100644 index 0000000000..e24ab99212 --- /dev/null +++ b/academic/bpp-phyl-omics/bpp-phyl-omics.info @@ -0,0 +1,10 @@ +PRGNAM="bpp-phyl-omics" +VERSION="git_2a61eee" +HOMEPAGE="http://biopp.univ-montp2.fr/" +DOWNLOAD="https://github.com/BioPP/bpp-phyl-omics/archive/2a61eee/bpp-phyl-omics-2a61eeee355cb9d7c5e774215307cd1876c8fbda.tar.gz" +MD5SUM="b08b3ed4ed6eb4e66249354240a189c6" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp-phyl bpp-seq-omics" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp-phyl-omics/slack-desc b/academic/bpp-phyl-omics/slack-desc new file mode 100644 index 0000000000..8709af393d --- /dev/null +++ b/academic/bpp-phyl-omics/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-phyl-omics: bpp-phyl (Bio++ Phylogenetic Omics Library) +bpp-phyl-omics: +bpp-phyl-omics: Contains the Bio++ Phylogenetic Omics Library +bpp-phyl-omics: +bpp-phyl-omics: Git: https://github.com/BioPP/bpp-phyl-omics +bpp-phyl-omics: +bpp-phyl-omics: +bpp-phyl-omics: +bpp-phyl-omics: +bpp-phyl-omics: +bpp-phyl-omics: -- cgit v1.2.3