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|
#!/bin/bash
# Slackware build script for ncbi-blast+
# This takes the place of ncbi-blast-plus (2013-2019), which just
# repackaged the binaries provided by upstream.
# Copyright 2013-2021 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=ncbi-blast+
VERSION=${VERSION:-2.13.0}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}
DIRNAM=ncbi-blast
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
set -e
rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf ${DIRNAM}-${VERSION}+-src
tar xvf $CWD/${DIRNAM}-${VERSION}+-src.tar.gz
cd ${DIRNAM}-${VERSION}+-src
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 {} \;
cd c++
# NOTE! Some additional options we could consider are:
# --without-autodep \ # automatic generation of dependencies (GNU make)
# --without-makefile-auto-update \ # do not auto-update generated makefiles
# --without-caution \ # proceed without asking when in doubt
# --without-boost \ # do not use Boost
# The full list of options is available in c++/src/build-system/configure
# Do not specify the libraries dir by the default way (--libdir=/lib${LIBDIRSUFFIX}),
# because the libs will not be included in the package.
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS -Wno-narrowing" \
./configure \
--prefix=/usr \
--libdir='${exec_prefix}'/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION \
--with-mt \
--with-dll \
--without-debug \
--without-downloaded-vdb \
--without-bdb \
--build=$ARCH-slackware-linux
# It does not seem to matter whether to use 'make all' and 'make install-toolkit',
# but let's have them here as a future reminder that these options exist.
#make all
#make prefix=$PKG/usr install-toolkit
make
make prefix=$PKG/usr install
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
# fix a few permissions
chmod 0644 $PKG/usr/include/ncbi-tools++/algo/dustmask/*.tex
chmod 0644 $PKG/usr/include/ncbi-tools++/objects/gbproj/*.{hpp,h}
chmod 0644 $PKG/usr/include/ncbi-tools++/objects/taxon3/*.hpp
chmod 0644 $PKG/usr/include/ncbi-tools++/objtools/edit/*.hpp
mkdir -p $PKG/usr/doc/$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
|
