slackbuilds/academic/vCAPS_coevolution/vCAPS_coevolution.SlackBuild

#!/bin/bash

# Slackware build script for vCAPS_coevolution

# Copyright 2020-2022 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.

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

PRGNAM=vCAPS_coevolution
VERSION=${VERSION:-2.0_2UN}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}

SRCNAM=caps
SRCVER=2.0
BINNAM=vCAPS

if [ -z "$ARCH" ]; then
  case "$( uname -m )" in
    i?86) ARCH=i586 ;;
    arm*) ARCH=arm ;;
       *) ARCH=$( uname -m ) ;;
  esac
fi

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}

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

LIBDIRPATH="-Wl,-rpath,/usr/lib${LIBDIRSUFFIX}/Bpp1.9"

set -e

rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf ${SRCNAM}${SRCVER}_src
unzip $CWD/${SRCNAM}2_src.zip
cd ${SRCNAM}${SRCVER}_src
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 {} \;

# This is needed for gcc in Slackware 14.2
sed -i "s:CC=g++ -g:CC=g++-5 -g -std=c++11:" Makefile

# Use our CFLAGS and the custom (legacy) lib path
sed -i "s:CFLAGS=:CFLAGS=$SLKCFLAGS $LIBDIRPATH:" Makefile

# Find the legacy bpp libraries
sed -i "s:-lbpp-phyl:-L/usr/lib${LIBDIRSUFFIX}/Bpp1.9 -lbpp-phyl:g" Makefile
sed -i "s:-lbpp-numcalc:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-numcalc:g" Makefile
sed -i "s:-lbpp-utils:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-utils:g" Makefile
sed -i "s:-lbpp-seq:-L/usr/lib64${LIBDIRSUFFIX}/Bpp1.9 -lbpp-seq:g" Makefile

# Rename the produced executable 
sed -i "s:-o caps:-o $BINNAM:" Makefile

# Use our patches
patch -p1 -i $CWD/01_caps_verbose.patch
patch -p1 -i $CWD/02_caps_sort_input.patch

# we already specified g++-5 above, so no need for this
#source /etc/profile.d/gcc5.sh

make all

# Install the binary produced from our patched source, as "vCAPS"
install -D -m755 $BINNAM $PKG/usr/bin/$BINNAM

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 $PKG/usr/share/$PRGNAM
cp -a sample structures trees TLR1.fa.out $PKG/usr/share/$PRGNAM

mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a \
  caps_manual.pdf \
  $PKG/usr/doc/$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