From cd2507649b2dcbc937fc9be5d9dd26da296b3be8 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Tue, 18 May 2021 16:14:18 +0300 Subject: academic/cufflinks: use binaries Signed-off-by: Willy Sudiarto Raharjo --- academic/cufflinks/README | 2 + academic/cufflinks/cufflinks.SlackBuild | 68 ++++++++++++--------------------- academic/cufflinks/cufflinks.info | 9 +++-- 3 files changed, 32 insertions(+), 47 deletions(-) (limited to 'academic') diff --git a/academic/cufflinks/README b/academic/cufflinks/README index 7afb95ee6e87d..5c851b1d276b7 100644 --- a/academic/cufflinks/README +++ b/academic/cufflinks/README @@ -11,6 +11,8 @@ Berkeley, Steven Salzberg's computational genomics group at the Institute of Genetic Medicine at Johns Hopkins University, and Barbara Wold's lab at Caltech. +NOTE: This just repackages the binaries provided from upstream. + Reference: Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and Barbara Wold, "Mapping and quantifying mammalian transcriptomes by diff --git a/academic/cufflinks/cufflinks.SlackBuild b/academic/cufflinks/cufflinks.SlackBuild index 33a09282e13c9..acc390420c546 100644 --- a/academic/cufflinks/cufflinks.SlackBuild +++ b/academic/cufflinks/cufflinks.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for cufflinks -# Copyright 2013-2019 Petar Petrov slackalaxy@gmail.com +# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -22,21 +22,22 @@ # OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -# With help from Archlinux AUR and Gentoo: -# https://aur.archlinux.org/packages/cufflinks/ -# http://euscan.iksaif.net/package/sci-biology/cufflinks/ +# For Slackware 15.0 I switched to just repackaging the upstream binaries. +# When I find a patch that fixes the build against boost and a bunch of other +# fixes, I will revert back to source build. Let's have ot like this for now. PRGNAM=cufflinks VERSION=${VERSION:-2.2.1} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then - case "$( uname -m )" in - i?86) ARCH=i586 ;; - arm*) ARCH=arm ;; - *) ARCH=$( uname -m ) ;; - esac + ARCH="$( uname -m )" +fi + +if [ "$ARCH" != "x86_64" ]; then + printf "\n\n$ARCH is not supported... \n" >&2 + exit 1 fi CWD=$(pwd) @@ -44,28 +45,14 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i586" ]; then - SLKCFLAGS="-O2 -march=i586 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "i686" ]; then - SLKCFLAGS="-O2 -march=i686 -mtune=i686" - LIBDIRSUFFIX="" -elif [ "$ARCH" = "x86_64" ]; then - SLKCFLAGS="-O2 -fPIC" - LIBDIRSUFFIX="64" -else - SLKCFLAGS="-O2" - LIBDIRSUFFIX="" -fi - set -e rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP -rm -rf $PRGNAM-$VERSION -tar xvf $CWD/$PRGNAM-$VERSION.tar.gz -cd $PRGNAM-$VERSION +rm -rf $PRGNAM-${VERSION}.Linux_${ARCH} +tar xvf $CWD/$PRGNAM-${VERSION}.Linux_${ARCH}.tar.gz +cd $PRGNAM-${VERSION}.Linux_${ARCH} chown -R root:root . find -L . \ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ @@ -73,22 +60,17 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -export EIGEN_CPPFLAGS="-I/usr/include/eigen3" - -CFLAGS="$SLKCFLAGS" \ -CXXFLAGS="$SLKCFLAGS" \ -./configure \ - --prefix=/usr \ - --libdir=/usr/lib${LIBDIRSUFFIX} \ - --sysconfdir=/etc \ - --disable-optim \ - --with-boost-libdir=/usr/lib${LIBDIRSUFFIX} \ - --localstatedir=/var \ - --mandir=/usr/man \ - --build=$ARCH-slackware-linux - -make -make install DESTDIR=$PKG +# Just in case... +sed -i "s:python:python2:" cuffmerge + +install -D -m755 cuffcompare $PKG/usr/bin/cuffcompare +install -D -m755 cuffdiff $PKG/usr/bin/cuffdiff +install -D -m755 cufflinks $PKG/usr/bin/cufflinks +install -D -m755 cuffmerge $PKG/usr/bin/cuffmerge +install -D -m755 cuffnorm $PKG/usr/bin/cuffnorm +install -D -m755 cuffquant $PKG/usr/bin/cuffquant +install -D -m755 gffread $PKG/usr/bin/gffread +install -D -m755 gtf_to_sam $PKG/usr/bin/gtf_to_sam find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/cufflinks/cufflinks.info b/academic/cufflinks/cufflinks.info index 6f858f0065cab..68816145439fe 100644 --- a/academic/cufflinks/cufflinks.info +++ b/academic/cufflinks/cufflinks.info @@ -1,10 +1,11 @@ PRGNAM="cufflinks" VERSION="2.2.1" HOMEPAGE="http://cufflinks.cbcb.umd.edu/" -DOWNLOAD="http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz" -MD5SUM="9a5ba7a7710cd864932cf205c17851f0" -DOWNLOAD_x86_64="" -MD5SUM_x86_64="" +DOWNLOAD="UNSUPPORTED" +MD5SUM="" +DOWNLOAD_x86_64="http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz" +MD5SUM_x86_64="7e693d182dcfda8aeef8523219ea9ea7" REQUIRES="samtools-legacy" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" + -- cgit v1.2.3