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slackbuilds_ponce/academic/EMBASSY/EMBASSY.SlackBuild
Petar Petrov 5313216267 academic/EMBASSY: Added (EMBOSS associated software) 
Signed-off-by: Niels Horn <niels.horn@slackbuilds.org>
2011-09-02 22:03:52 -03:00

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#!/bin/sh
# Slackware build script for EMBASSY
# Written by Petar Petrov, <ppetrov@paju.oulu.fi> and
# hereby submitted to the public domain
# THIS SLACKBUILD IS DISTRIBUTETD IN THE HOPE OF BEING
# USEFUL BUT WITHOUT ANY WARRANTY. THE AUTHOR IS _NOT_
# RESPONSIBLE FOR ANY DAMAGE OR DATA LOSS CAUSED BY IT.
PRGNAM=EMBASSY
VERSION=${VERSION:-6.4.0} # Keep this the same as the version of EMBOSS.
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i486 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
fi
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i486" ]; then
SLKCFLAGS="-O2 -march=i486 -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
mkdir $TMP/$PRGNAM-$VERSION
# Build CBSTOOLS
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/CBSTOOLS-*.tar.gz
cd CBSTOOLS-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/CBSTOOLS \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build CLUSTALOMEGA
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/CLUSTALOMEGA-*.tar.gz
cd CLUSTALOMEGA-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/CLUSTALOMEGA \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build DOMAINATRIX
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/DOMAINATRIX-*.tar.gz
cd DOMAINATRIX-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/DOMAINATRIX \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build DOMALIGN
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/DOMALIGN-*.tar.gz
cd DOMALIGN-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/DOMALIGN \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build DOMSEARCH
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/DOMSEARCH-*.tar.gz
cd DOMSEARCH-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/DOMSEARCH \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build EMNU
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/EMNU-*.tar.gz
cd EMNU-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/EMNU \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build ESIM4
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/ESIM4-*.tar.gz
cd ESIM4-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/ESIM4 \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build HMMER
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/HMMER-*.tar.gz
cd HMMER-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/HMMER \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build IPRSCAN
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/IPRSCAN-*.tar.gz
cd IPRSCAN-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/IPRSCAN \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build MEME
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/MEME-*.tar.gz
cd MEME-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MEME \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build MSE
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/MSE-*.tar.gz
cd MSE-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MSE \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build MYEMBOSS
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/MYEMBOSS-*.tar.gz
cd MYEMBOSS-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSS \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build MYEMBOSSDEMO
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/MYEMBOSSDEMO-*.tar.gz
cd MYEMBOSSDEMO-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/MYEMBOSSDEMO \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build PHYLIPNEW
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/PHYLIPNEW-*.tar.gz
cd PHYLIPNEW-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/PHYLIPNEW \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build SIGNATURE
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/SIGNATURE-*.tar.gz
cd SIGNATURE-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/SIGNATURE \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build STRUCTURE
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/STRUCTURE-*.tar.gz
cd STRUCTURE-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/STRUCTURE \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build TOPO
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/TOPO-*.tar.gz
cd TOPO-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/TOPO \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
# Build VIENNA
cd $TMP/$PRGNAM-$VERSION
tar xvf $CWD/VIENNA-*.tar.gz
cd VIENNA-*
chown -R root:root .
find . \
\( -perm 777 -o -perm 775 -o -perm 711 -o -perm 555 -o -perm 511 \) \
-exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
-exec chmod 644 {} \;
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
--sysconfdir=/etc \
--localstatedir=/var \
--mandir=/usr/man \
--docdir=/usr/doc/$PRGNAM-$VERSION/VIENNA \
--build=$ARCH-slackware-linux
make
make DESTDIR=$PKG install
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
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/CONTENTS > $PKG/usr/doc/$PRGNAM-$VERSION/CONTENTS
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:-tgz}
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