mirror of
https://github.com/Ponce/slackbuilds
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118 lines
4 KiB
Bash
118 lines
4 KiB
Bash
#!/bin/sh
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# Slackware build script for ncbi-blast-plus
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# Copyright 2013-2015 Petar Petrov, petar.petrov@student.oulu.fi
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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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PRGNAM=ncbi-blast-plus
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VERSION=${VERSION:-2.2.31}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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SRCNAM=ncbi-blast
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SRCVER=2.2.31+
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if [ -z "$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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CWD=$(pwd)
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TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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set -e
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# Check for host architecture. Distribution of 32bit binaries has been
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# dropped from NCBI. For more information, please read:
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# http://www.ncbi.nlm.nih.gov/mailman/pipermail/blast-announce/2015q2/000112.html
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if [ "$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=$SRCNAM-$SRCVER-$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 $SRCNAM-$SRCVER
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tar xvf $CWD/$TARNAME.tar.gz
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cd $SRCNAM-$SRCVER
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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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# Install the precompiled binaries.
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cd bin
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install -D -m755 blast_formatter $PKG/usr/bin/blast_formatter
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install -D -m755 blastdb_aliastool $PKG/usr/bin/blastdb_aliastool
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install -D -m755 blastdbcheck $PKG/usr/bin/blastdbcheck
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install -D -m755 blastdbcmd $PKG/usr/bin/blastdbcmd
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install -D -m755 blastn $PKG/usr/bin/blastn
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install -D -m755 blastp $PKG/usr/bin/blastp
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install -D -m755 blastx $PKG/usr/bin/blastx
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install -D -m755 convert2blastmask $PKG/usr/bin/convert2blastmask
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install -D -m755 deltablast $PKG/usr/bin/deltablast
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install -D -m755 dustmasker $PKG/usr/bin/dustmasker
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install -D -m755 legacy_blast.pl $PKG/usr/bin/legacy_blast.pl
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install -D -m755 makeblastdb $PKG/usr/bin/makeblastdb
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install -D -m755 makembindex $PKG/usr/bin/makembindex
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install -D -m755 makeprofiledb $PKG/usr/bin/makeprofiledb
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install -D -m755 psiblast $PKG/usr/bin/psiblast
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install -D -m755 rpsblast $PKG/usr/bin/rpsblast
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install -D -m755 rpstblastn $PKG/usr/bin/rpstblastn
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install -D -m755 segmasker $PKG/usr/bin/segmasker
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install -D -m755 tblastn $PKG/usr/bin/tblastn
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install -D -m755 tblastx $PKG/usr/bin/tblastx
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install -D -m755 update_blastdb.pl $PKG/usr/bin/update_blastdb.pl
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install -D -m755 windowmasker $PKG/usr/bin/windowmasker
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cd ..
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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-$VERSION
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cp -a \
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ChangeLog LICENSE README doc/README.txt \
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$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:-tgz}
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