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academic/cufflinks: use binaries
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
f703b64e18
commit
cd2507649b
3 changed files with 31 additions and 46 deletions
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@ -11,6 +11,8 @@ Berkeley, Steven Salzberg's computational genomics group at the
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Institute of Genetic Medicine at Johns Hopkins University, and Barbara
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Wold's lab at Caltech.
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NOTE: This just repackages the binaries provided from upstream.
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Reference:
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Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and
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Barbara Wold, "Mapping and quantifying mammalian transcriptomes by
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@ -2,7 +2,7 @@
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# Slackware build script for cufflinks
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# Copyright 2013-2019 Petar Petrov slackalaxy@gmail.com
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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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@ -22,21 +22,22 @@
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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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# With help from Archlinux AUR and Gentoo:
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# https://aur.archlinux.org/packages/cufflinks/
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# http://euscan.iksaif.net/package/sci-biology/cufflinks/
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# For Slackware 15.0 I switched to just repackaging the upstream binaries.
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# When I find a patch that fixes the build against boost and a bunch of other
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# fixes, I will revert back to source build. Let's have ot like this for now.
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PRGNAM=cufflinks
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VERSION=${VERSION:-2.2.1}
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BUILD=${BUILD:-1}
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BUILD=${BUILD:-2}
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TAG=${TAG:-_SBo}
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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=$( uname -m ) ;;
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esac
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ARCH="$( uname -m )"
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fi
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if [ "$ARCH" != "x86_64" ]; then
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printf "\n\n$ARCH is not supported... \n" >&2
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exit 1
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fi
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CWD=$(pwd)
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@ -44,28 +45,14 @@ TMP=${TMP:-/tmp/SBo}
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PKG=$TMP/package-$PRGNAM
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OUTPUT=${OUTPUT:-/tmp}
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if [ "$ARCH" = "i586" ]; then
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SLKCFLAGS="-O2 -march=i586 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "i686" ]; then
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SLKCFLAGS="-O2 -march=i686 -mtune=i686"
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LIBDIRSUFFIX=""
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elif [ "$ARCH" = "x86_64" ]; then
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SLKCFLAGS="-O2 -fPIC"
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LIBDIRSUFFIX="64"
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else
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SLKCFLAGS="-O2"
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LIBDIRSUFFIX=""
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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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rm -rf $PRGNAM-${VERSION}.Linux_${ARCH}
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tar xvf $CWD/$PRGNAM-${VERSION}.Linux_${ARCH}.tar.gz
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cd $PRGNAM-${VERSION}.Linux_${ARCH}
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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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@ -73,22 +60,17 @@ find -L . \
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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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export EIGEN_CPPFLAGS="-I/usr/include/eigen3"
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# Just in case...
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sed -i "s:python:python2:" cuffmerge
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CFLAGS="$SLKCFLAGS" \
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CXXFLAGS="$SLKCFLAGS" \
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./configure \
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--prefix=/usr \
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--libdir=/usr/lib${LIBDIRSUFFIX} \
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--sysconfdir=/etc \
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--disable-optim \
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--with-boost-libdir=/usr/lib${LIBDIRSUFFIX} \
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--localstatedir=/var \
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--mandir=/usr/man \
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--build=$ARCH-slackware-linux
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make
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make install DESTDIR=$PKG
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install -D -m755 cuffcompare $PKG/usr/bin/cuffcompare
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install -D -m755 cuffdiff $PKG/usr/bin/cuffdiff
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install -D -m755 cufflinks $PKG/usr/bin/cufflinks
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install -D -m755 cuffmerge $PKG/usr/bin/cuffmerge
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install -D -m755 cuffnorm $PKG/usr/bin/cuffnorm
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install -D -m755 cuffquant $PKG/usr/bin/cuffquant
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install -D -m755 gffread $PKG/usr/bin/gffread
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install -D -m755 gtf_to_sam $PKG/usr/bin/gtf_to_sam
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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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@ -1,10 +1,11 @@
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PRGNAM="cufflinks"
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VERSION="2.2.1"
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HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
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DOWNLOAD="http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz"
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MD5SUM="9a5ba7a7710cd864932cf205c17851f0"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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DOWNLOAD="UNSUPPORTED"
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MD5SUM=""
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DOWNLOAD_x86_64="http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz"
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MD5SUM_x86_64="7e693d182dcfda8aeef8523219ea9ea7"
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REQUIRES="samtools-legacy"
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MAINTAINER="Petar Petrov"
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EMAIL="slackalaxy@gmail.com"
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