diff --git a/academic/bpp1.9-seq/README b/academic/bpp1.9-seq/README deleted file mode 100644 index eaeb91d929..0000000000 --- a/academic/bpp1.9-seq/README +++ /dev/null @@ -1,10 +0,0 @@ -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) Seq 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-seq/bpp1.9-seq.SlackBuild b/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild deleted file mode 100644 index 4d076f1a69..0000000000 --- a/academic/bpp1.9-seq/bpp1.9-seq.SlackBuild +++ /dev/null @@ -1,120 +0,0 @@ -#!/bin/bash - -# Slackware build script for bpp1.9-seq - -# Copyright 2020-2021 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=bpp1.9-seq -SRCNAM=bpp-seq -VERSION=${VERSION:-1.7.0} -BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} -PKGTYPE=${PKGTYPE:-tgz} - -if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac -fi - -# If the variable PRINT_PACKAGE_NAME is set, then this script will report what -# the name of the created package would be, and then exit. This information -# could be useful to other scripts. -if [ ! -z "${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 [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - -# This is needed for vCAPS to find its libraries at runtime. Thanks Urchlay! -LIBDIRPATH="-Wl,-rpath,/usr/lib${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${LIBDIRSUFFIX}/Bpp1.9/:g" Seq.spec - -mkdir -p build -cd build - cmake \ - -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS $LIBDIRPATH" \ - -DCMAKE_INSTALL_PREFIX=/usr \ - -DCMAKE_BUILD_TYPE=Release .. - - sed -i "s:/lib/:/lib${LIBDIRSUFFIX}/Bpp1.9/:g" Seq/cmake_install.cmake - sed -i "s:/lib\b:/lib${LIBDIRSUFFIX}/Bpp1.9:g" Seq/cmake_install.cmake - - make - make DESTDIR=$PKG install -cd .. - -# Remove static lib -rm -f $PKG/usr/lib64/Bpp1.9/libbpp-seq.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 diff --git a/academic/bpp1.9-seq/bpp1.9-seq.info b/academic/bpp1.9-seq/bpp1.9-seq.info deleted file mode 100644 index 35b6d40f95..0000000000 --- a/academic/bpp1.9-seq/bpp1.9-seq.info +++ /dev/null @@ -1,10 +0,0 @@ -PRGNAM="bpp1.9-seq" -VERSION="1.7.0" -HOMEPAGE="http://biopp.univ-montp2.fr/" -DOWNLOAD="http://biopp.univ-montp2.fr/repos/sources/bpp-seq-1.7.0.tar.gz" -MD5SUM="4256293637ac4131c0d030f5265b8b8b" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" -REQUIRES="bpp1.9-numcalc" -MAINTAINER="Petar Petrov" -EMAIL="slackalaxy@gmail.com" diff --git a/academic/bpp1.9-seq/slack-desc b/academic/bpp1.9-seq/slack-desc deleted file mode 100644 index bd154ce1f1..0000000000 --- a/academic/bpp1.9-seq/slack-desc +++ /dev/null @@ -1,19 +0,0 @@ -# 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-seq: bpp1.9-seq (Bio++ 1.9 Seq Library) -bpp1.9-seq: -bpp1.9-seq: Contains the Bio++ 1.9 Seq Library. -bpp1.9-seq: -bpp1.9-seq: -bpp1.9-seq: -bpp1.9-seq: -bpp1.9-seq: -bpp1.9-seq: -bpp1.9-seq: -bpp1.9-seq: