mirror of
https://github.com/Ponce/slackbuilds
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127 lines
4.4 KiB
Bash
127 lines
4.4 KiB
Bash
#!/bin/bash
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# Slackware build script for STAR
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# Copyright 2018-2022 Rob van Nues <sborg63@disroot.org>
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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=STAR
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VERSION=${VERSION:-2.7.10a}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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PKGTYPE=${PKGTYPE:-tgz}
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# This script is set for processors that support "Advanced Vector Extensions",
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# (AVX), included since 2008 in Intel processors (Sandy Bridge) and since 2011
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# in AMD cpus (Bulldozer). AVX is an implementation of "Single Instruction
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# stream-Multiple Data streams" (SIMD) to process vector type data.
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# If no AVX (`cat /proc/cpuinfo | grep 'avx'`) is present, specify the
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# available SIMD architecture (https://en.wikichip.org/wiki/x86/extensions),
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# e.g. with "Streaming SIMD Extensions" use 'sse', and uncomment the next line.
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#SIMD=${SIMD:-sse}; echo "Using ${SIMD} as SIMD"
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if [ -z "$ARCH" ]; then
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case "$( uname -m )" in
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i?86) ARCH=i586 ;;
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arm*) ARCH=arm ;;
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*) ARCH=$( 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=${OUTPUT:-/tmp}
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if [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC -fsigned-char"
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LIBDIRSUFFIX="64"
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else
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echo "Sorry, this program does not run/compile on your architecture ($ARCH)"
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exit 0
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fi
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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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tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
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cd $PRGNAM-$VERSION
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -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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# for using shared, externally-installed htslib (as done on debian)
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#rm -rf htslib
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# from https://salsa.debian.org/med-team/rna-star/tree/master/debian/patches
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#patch < $CWD/donotuse_own_htslib.patch
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# but Alex Dobin, the developer of STAR does not advise this due to hacks he made in htslib
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# https://github.com/alexdobin/STAR/issues/351
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# https://github.com/alexdobin/STAR/issues/447
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#so let's forget about this for now
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#For processors that do not support AVX extensions, specify the target SIMD architecture
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#make STAR CXXFLAGS_SIMD=sse
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cd source
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if [ ! -z "${SIMD}" ]; then
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echo "make with CXXFLAG_SIMD=${SIMD}"
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make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS" CXXFLAGS_SIMD="$SIMD"
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else
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echo "default make"
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make ${PRGNAM} CFLAGS="$SLKCFLAGS" CXXFLAGSextra="$SLKCFLAGS"
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fi
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mkdir -p $PKG/usr/bin
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install -Dm755 $PRGNAM "$PKG/usr/bin/${PRGNAM}"
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#make clean
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#make ${PRGNAM}long CXXFLAGSextra="$CXXFLAGS"
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#install -Dm755 ${PRGNAM}long "$PKG/usr/bin/${PRGNAM}long"
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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-$VERSION
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cp -a \
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source/parametersDefault doc/${PRGNAM}manual.pdf CHANGES.md LICENSE README.md RELEASEnotes.md \
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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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