diff options
author | Petar Petrov <slackalaxy@gmail.com> | 2022-09-08 07:14:21 +0100 |
---|---|---|
committer | Dave Woodfall <dave@slackbuilds.org> | 2022-09-08 08:11:04 +0100 |
commit | 2b4673188b7e9bc3f2844b847388c5be1693e6be (patch) | |
tree | 5304ba35eb55912d7a408a4cffd1265f4188277c /academic/bppsuite | |
parent | 0b01583f8de8132f8b93314a2c503a5f317a43cc (diff) |
academic/bppsuite: Added (Bio++ program suite)
Signed-off-by: Dave Woodfall <dave@slackbuilds.org>
Diffstat (limited to 'academic/bppsuite')
-rw-r--r-- | academic/bppsuite/README | 11 | ||||
-rw-r--r-- | academic/bppsuite/bppsuite.SlackBuild | 113 | ||||
-rw-r--r-- | academic/bppsuite/bppsuite.info | 10 | ||||
-rw-r--r-- | academic/bppsuite/slack-desc | 19 |
4 files changed, 153 insertions, 0 deletions
diff --git a/academic/bppsuite/README b/academic/bppsuite/README new file mode 100644 index 0000000000000..cc877ea40b0af --- /dev/null +++ b/academic/bppsuite/README @@ -0,0 +1,11 @@ +Bio++ program suite + +The Bio++ Program Suite is a package of programs using the Bio++ +libraries and dedicated to Phylogenetics and Molecular Evolution. All +programs are independent, but can be combined to perform rather +complex analyses. These programs use the interface helper tools of the +libraries, and hence share the same syntax. They also have several +options in common, which may also be shared by third-party software. + +Detailed documentation can be found (as PDF and HTML) here: +https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 diff --git a/academic/bppsuite/bppsuite.SlackBuild b/academic/bppsuite/bppsuite.SlackBuild new file mode 100644 index 0000000000000..4e4bc8c2d2bad --- /dev/null +++ b/academic/bppsuite/bppsuite.SlackBuild @@ -0,0 +1,113 @@ +#!/bin/bash + +# Slackware build script for bppsuite + +# Copyright 2017-2022 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=bppsuite +VERSION=${VERSION:-2.4.1} +BUILD=${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 + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd $PRGNAM-$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 {} \; + +mkdir -p build +cd build + cmake \ + -DCMAKE_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release .. + make + make install DESTDIR=$PKG +cd .. + +# Place man pages to their proper location +mkdir -p $PKG/usr/man/man1 +mv $PKG/usr/share/man/man1/* $PKG/usr/man/man1 + +# Place info pages to their proper location +mkdir -p $PKG/usr/info +mv $PKG/usr/share/info/* $PKG/usr/info +rm -rf $PKG/usr/share + +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 + +rm -f $PKG/usr/info/dir +gzip -9 $PKG/usr/info/*.info* + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a AUTHORS.txt ChangeLog COPYING.txt README.md $PKG/usr/doc/$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/bppsuite/bppsuite.info b/academic/bppsuite/bppsuite.info new file mode 100644 index 0000000000000..97626a2bff0c0 --- /dev/null +++ b/academic/bppsuite/bppsuite.info @@ -0,0 +1,10 @@ +PRGNAM="bppsuite" +VERSION="2.4.1" +HOMEPAGE="https://github.com/BioPP/" +DOWNLOAD="https://github.com/BioPP/bppsuite/archive/v2.4.1/bppsuite-2.4.1.tar.gz" +MD5SUM="d254ffd9e121b408aed36f49e62920d1" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="bpp-seq-omics bpp-phyl-omics bpp-popgen" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/bppsuite/slack-desc b/academic/bppsuite/slack-desc new file mode 100644 index 0000000000000..8419aa4f1e790 --- /dev/null +++ b/academic/bppsuite/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------------------------------------------------------| +bppsuite: bppsuite (Bio++ program suite) +bppsuite: +bppsuite: The Bio++ Program Suite is a package of programs using the Bio++ +bppsuite: libraries and dedicated to Phylogenetics and Molecular Evolution. +bppsuite: All programs are independent, but can be combined to perform +bppsuite: rather complex analyses. These programs use the interface helper +bppsuite: tools of the libraries, and hence share the same syntax. They also +bppsuite: have several options in common, which may also be shared by third- +bppsuite: party software. +bppsuite: +bppsuite: Git: https://github.com/BioPP/bppsuite |