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academic/bpp1.9-seq: Removed (ftb + no active maintainer).
Signed-off-by: Matteo Bernardini <ponce@slackbuilds.org>
This commit is contained in:
Matteo Bernardini
Robby Workman
parent
9f84b277cd
commit
2a8e2c8f35
4 changed files with 0 additions and 159 deletions
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Bio++ is a set of C++ libraries for Bioinformatics, including sequence
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analysis, phylogenetics, molecular evolution and population genetics.
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Bio++ is Object Oriented and is designed to be both easy to use and
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computer efficient. Bio++ intends to help programmers to write
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computer expensive programs, by providing them a set of re-usable
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tools.
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This contains the Bio++ 1.9 (April 2010) Seq Library. It can be
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installed along the current Bio++ suite libraries, however they better
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not be present at compile time.
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#!/bin/bash
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# Slackware build script for bpp1.9-seq
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# Copyright 2020-2021 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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# permitted provided that the following conditions are met:
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#
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# 1. Redistributions of this script must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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#
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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cd $(dirname $0) ; CWD=$(pwd)
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PRGNAM=bpp1.9-seq
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SRCNAM=bpp-seq
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VERSION=${VERSION:-1.7.0}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( uname -m ) ;;
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esac
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fi
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# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
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# the name of the created package would be, and then exit. This information
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# could be useful to other scripts.
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if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
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echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
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exit 0
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fi
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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fi
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# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay!
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LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9"
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set -e
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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $SRCNAM-$VERSION
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tar xvf $CWD/$SRCNAM-$VERSION.tar.gz
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cd $SRCNAM-$VERSION
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Use custom install place, so libs can coexist with latest bpp
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export PATH="/usr/lib${LIBDIRSUFFIX}/Bpp1.9/:$PATH"
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sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Seq.spec
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mkdir -p build
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cd build
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cmake \
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-DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \
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-DCMAKE_INSTALL_PREFIX=/usr \
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-DCMAKE_BUILD_TYPE=Release ..
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sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Seq/cmake_install.cmake
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sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Seq/cmake_install.cmake
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make
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make DESTDIR=$PKG install
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cd ..
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# Remove static lib
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rm -f $PKG/usr/lib64/Bpp1.9/libbpp-seq.a
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
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cp -a \
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AUTHORS ChangeLog COPYING INSTALL \
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$PKG/usr/doc/$PRGNAM-$VERSION
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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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mkdir -p $PKG/install
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cat $CWD/slack-desc > $PKG/install/slack-desc
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cd $PKG
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/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
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@ -1,10 +0,0 @@
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PRGNAM="bpp1.9-seq"
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VERSION="1.7.0"
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HOMEPAGE="http://biopp.univ-montp2.fr/"
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DOWNLOAD="http://biopp.univ-montp2.fr/repos/sources/bpp-seq-1.7.0.tar.gz"
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MD5SUM="4256293637ac4131c0d030f5265b8b8b"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="bpp1.9-numcalc"
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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@ -1,19 +0,0 @@
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# HOW TO EDIT THIS FILE:
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# The "handy ruler" below makes it easier to edit a package description.
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# Line up the first '|' above the ':' following the base package name, and
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# the '|' on the right side marks the last column you can put a character in.
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# You must make exactly 11 lines for the formatting to be correct. It's also
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# customary to leave one space after the ':' except on otherwise blank lines.
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|-----handy-ruler------------------------------------------------------|
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bpp1.9-seq: bpp1.9-seq (Bio++ 1.9 Seq Library)
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bpp1.9-seq:
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bpp1.9-seq: Contains the Bio++ 1.9 Seq Library.
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bpp1.9-seq:
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bpp1.9-seq:
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bpp1.9-seq:
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bpp1.9-seq:
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bpp1.9-seq:
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bpp1.9-seq:
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bpp1.9-seq:
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bpp1.9-seq:
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