121 lines
3.7 KiB
Bash
121 lines
3.7 KiB
Bash
#!/bin/bash
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# Slackware build script for ncbi-blast
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# Copyright 2013-2021 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=ncbi-blast
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VERSION=${VERSION:-2.2.26}
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BUILD=${BUILD:-2}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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SRCNAM=blast
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i386 ;;
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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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set -e
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if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then
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printf "\n\n$ARCH is not supported... \n"
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exit 1
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fi
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# Determine the source arch
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if [ "$ARCH" = "x86_64" ]; then
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SRCARCH="x64"
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else
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SRCARCH="ia32"
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fi
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# Construct the tarball name
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TARNAME=$SRCNAM-$VERSION-$SRCARCH-linux
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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 $CWD/$TARNAME.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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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
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-exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
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-exec chmod 644 {} \;
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# Install the precompiled binaries. Change the name of rpsblast and
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# seedtop as they are also part of the ncbi-blast+ package.
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cd bin
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install -D -m755 bl2seq $PKG/usr/bin/bl2seq
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install -D -m755 blastall $PKG/usr/bin/blastall
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install -D -m755 blastclust $PKG/usr/bin/blastclust
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install -D -m755 blastpgp $PKG/usr/bin/blastpgp
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install -D -m755 copymat $PKG/usr/bin/copymat
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install -D -m755 fastacmd $PKG/usr/bin/fastacmd
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install -D -m755 formatdb $PKG/usr/bin/formatdb
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install -D -m755 formatrpsdb $PKG/usr/bin/formatrpsdb
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install -D -m755 impala $PKG/usr/bin/impala
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install -D -m755 makemat $PKG/usr/bin/makemat
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install -D -m755 megablast $PKG/usr/bin/megablast
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install -D -m755 rpsblast $PKG/usr/bin/rpsblast-legacy
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install -D -m755 seedtop $PKG/usr/bin/seedtop-legacy
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cd ..
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# Copy data dir
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mkdir -p $PKG/usr/share/$PRGNAM
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cp -a data $PKG/usr/share/$PRGNAM
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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-$VERSION
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cp -a \
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doc/* VERSION \
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$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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