slackbuilds/academic/ncbi-blast/ncbi-blast.SlackBuild

#!/bin/bash

# Slackware build script for ncbi-blast

# 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.

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

PRGNAM=ncbi-blast
VERSION=${VERSION:-2.2.26}
BUILD=${BUILD:-2}
TAG=${TAG:-_SBo}
PKGTYPE=${PKGTYPE:-tgz}

SRCNAM=blast

if [ -z "$ARCH" ]; then
  case "$( uname -m )" in
    i?86) ARCH=i386 ;;
    arm*) ARCH=arm ;;
       *) ARCH=$( uname -m ) ;;
  esac
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

if [ "$ARCH" != "i386" ] && [ "$ARCH" != "x86_64" ]; then
  printf "\n\n$ARCH is not supported... \n"
  exit 1
fi

# Determine the source arch
if [ "$ARCH" = "x86_64" ]; then
  SRCARCH="x64"
else
  SRCARCH="ia32"
fi

# Construct the tarball name
TARNAME=$SRCNAM-$VERSION-$SRCARCH-linux

rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf $SRCNAM-$VERSION
tar xvf $CWD/$TARNAME.tar.gz
cd $SRCNAM-$VERSION
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 \
 \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
 -exec chmod 644 {} \;

# Install the precompiled binaries. Change the name of rpsblast and
# seedtop as they are also part of the ncbi-blast+ package.
cd bin
install -D -m755 bl2seq	$PKG/usr/bin/bl2seq
install -D -m755 blastall $PKG/usr/bin/blastall
install -D -m755 blastclust $PKG/usr/bin/blastclust
install -D -m755 blastpgp $PKG/usr/bin/blastpgp
install -D -m755 copymat $PKG/usr/bin/copymat
install -D -m755 fastacmd $PKG/usr/bin/fastacmd
install -D -m755 formatdb $PKG/usr/bin/formatdb
install -D -m755 formatrpsdb $PKG/usr/bin/formatrpsdb
install -D -m755 impala	$PKG/usr/bin/impala
install -D -m755 makemat $PKG/usr/bin/makemat
install -D -m755 megablast $PKG/usr/bin/megablast
install -D -m755 rpsblast $PKG/usr/bin/rpsblast-legacy
install -D -m755 seedtop $PKG/usr/bin/seedtop-legacy
cd ..

# Copy data dir
mkdir -p $PKG/usr/share/$PRGNAM
cp -a data $PKG/usr/share/$PRGNAM

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 \
  doc/* VERSION \
  $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild

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