mirror of
https://github.com/Ponce/slackbuilds
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6bc47f9735
Signed-off-by: Dave Woodfall <dave@slackbuilds.org> Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
88 lines
2.9 KiB
Bash
88 lines
2.9 KiB
Bash
#!/bin/bash
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# Slackware build script for snpEff
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# Copyright 2015-2022 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=snpEff
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VERSION=${VERSION:-4.3t}
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SRCVER=${SRCVER:-v4_3t}
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BUILD=${BUILD:-2}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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ARCH=noarch
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# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
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# the name of the created package would be, and then exit. This information
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# could be useful to other scripts.
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if [ ! -z "${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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rm -rf $PKG
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mkdir -p $TMP $PKG $OUTPUT
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cd $TMP
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rm -rf $PRGNAM-$VERSION
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mkdir -p $PRGNAM-$VERSION
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cd $PRGNAM-$VERSION
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unzip $CWD/${PRGNAM}_${SRCVER}_core.zip
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cd $PRGNAM
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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 -D -m755 $PRGNAM.jar $PKG/usr/share/java/$PRGNAM/$PRGNAM.jar
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install -D -m755 SnpSift.jar $PKG/usr/share/java/$PRGNAM/SnpSift.jar
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cp -a examples galaxy scripts $PRGNAM.config \
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$PKG/usr/share/java/$PRGNAM
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mkdir -p $PKG/usr/bin
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cd $PKG/usr/bin
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ln -s ../share/java/$PRGNAM/snpEff.jar
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ln -s ../share/java/$PRGNAM/SnpSift.jar
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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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cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
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cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
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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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