slackbuilds/academic/cufflinks/cufflinks.SlackBuild

#!/bin/bash

# Slackware build script for cufflinks

# Copyright 2013-2021 Petar Petrov slackalaxy@gmail.com
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
# permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
#    notice, this list of conditions and the following disclaimer.
#
#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

# 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.

cd $(dirname $0) ; CWD=$(pwd)

PRGNAM=cufflinks
VERSION=${VERSION:-2.2.1}
BUILD=${BUILD:-2}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}

if [ -z "$ARCH" ]; then
  ARCH="$( uname -m )"
fi

if [ "$ARCH" != "x86_64" ]; then
  printf "\n\n$ARCH is not supported... \n" >&2
  exit 1
fi

# If the variable PRINT_PACKAGE_NAME is set, then this script will report what
# the name of the created package would be, and then exit. This information
# could be useful to other scripts.
if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
  echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
  exit 0
fi

TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}

set -e

rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
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 . \
 \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
  -o -perm 511 \) -exec chmod 755 {} \; -o \
 \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
 -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;

# 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

mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
  AUTHORS LICENSE README \
  $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References

mkdir -p $PKG/install
cat $CWD/slack-desc > $PKG/install/slack-desc

cd $PKG
/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE