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|
#!/bin/sh
# Slackware build script for ncbi-blast-plus
# Copyright 2013-2015 Petar Petrov, petar.petrov@student.oulu.fi
# 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=ncbi-blast-plus
VERSION=${VERSION:-2.2.31}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
SRCNAM=ncbi-blast
SRCVER=2.2.31+
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i386 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
fi
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
set -e
# Check for host architecture. Distribution of 32bit binaries has been
# dropped from NCBI. For more information, please read:
# http://www.ncbi.nlm.nih.gov/mailman/pipermail/blast-announce/2015q2/000112.html
if [ "$ARCH" != "x86_64" ]; then
printf "\n\n$ARCH is not supported... \n"
exit 1
fi
# Determine the source arch
if [ "$ARCH" = "x86_64" ]; then
SRCARCH="x64"
else
SRCARCH="ia32"
fi
# Construct the tarball name
TARNAME=$SRCNAM-$SRCVER-$SRCARCH-linux
rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $SRCNAM-$SRCVER
tar xvf $CWD/$TARNAME.tar.gz
cd $SRCNAM-$SRCVER
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 {} \;
# Install the precompiled binaries.
cd bin
install -D -m755 blast_formatter $PKG/usr/bin/blast_formatter
install -D -m755 blastdb_aliastool $PKG/usr/bin/blastdb_aliastool
install -D -m755 blastdbcheck $PKG/usr/bin/blastdbcheck
install -D -m755 blastdbcmd $PKG/usr/bin/blastdbcmd
install -D -m755 blastn $PKG/usr/bin/blastn
install -D -m755 blastp $PKG/usr/bin/blastp
install -D -m755 blastx $PKG/usr/bin/blastx
install -D -m755 convert2blastmask $PKG/usr/bin/convert2blastmask
install -D -m755 deltablast $PKG/usr/bin/deltablast
install -D -m755 dustmasker $PKG/usr/bin/dustmasker
install -D -m755 legacy_blast.pl $PKG/usr/bin/legacy_blast.pl
install -D -m755 makeblastdb $PKG/usr/bin/makeblastdb
install -D -m755 makembindex $PKG/usr/bin/makembindex
install -D -m755 makeprofiledb $PKG/usr/bin/makeprofiledb
install -D -m755 psiblast $PKG/usr/bin/psiblast
install -D -m755 rpsblast $PKG/usr/bin/rpsblast
install -D -m755 rpstblastn $PKG/usr/bin/rpstblastn
install -D -m755 segmasker $PKG/usr/bin/segmasker
install -D -m755 tblastn $PKG/usr/bin/tblastn
install -D -m755 tblastx $PKG/usr/bin/tblastx
install -D -m755 update_blastdb.pl $PKG/usr/bin/update_blastdb.pl
install -D -m755 windowmasker $PKG/usr/bin/windowmasker
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 \
ChangeLog LICENSE README doc/README.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}
|
