From cd2507649b2dcbc937fc9be5d9dd26da296b3be8 Mon Sep 17 00:00:00 2001
From: Petar Petrov <slackalaxy@gmail.com>
Date: Tue, 18 May 2021 16:14:18 +0300
Subject: academic/cufflinks: use binaries

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/cufflinks/README               |  2 +
 academic/cufflinks/cufflinks.SlackBuild | 68 ++++++++++++---------------------
 academic/cufflinks/cufflinks.info       |  9 +++--
 3 files changed, 32 insertions(+), 47 deletions(-)

(limited to 'academic/cufflinks')

diff --git a/academic/cufflinks/README b/academic/cufflinks/README
index 7afb95ee6e..5c851b1d27 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 33a09282e1..acc390420c 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 6f858f0065..6881614543 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"
+
-- 
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