Browse Source

ap/EMBOSS: Added.

slackware-14.2
Damien Goutte-Gattat 13 years ago
parent
commit
f82813a458
  1. 1
      ap/EMBOSS/EMBOSS-6.0.1.tar.gz.sha1
  2. 126
      ap/EMBOSS/EMBOSS.SlackBuild
  3. 13
      ap/EMBOSS/slack-desc

1
ap/EMBOSS/EMBOSS-6.0.1.tar.gz.sha1

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ea6fa6e1e4222bc57e748a4d674d72d9b03475dd EMBOSS-6.0.1.tar.gz

126
ap/EMBOSS/EMBOSS.SlackBuild

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#!/bin/bash
# Build script for Slackware
# Damien Goutte-Gattat "gouttegd" < damien.goutte-gattat at e.ujf-grenoble.fr >
#
# Redistribution and use of this script, with or without modifications, 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.
#
# Latest EMBOSS sourcecode is available at:
# http://emboss.sourceforge.net/
# Source package infos
NAMESRC=${NAMESRC:-EMBOSS}
VERSION=${VERSION:-6.0.1}
ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
WGET=${WGET:-ftp://emboss.open-bio.org/pub/EMBOSS/$ARCHIVE}
# Built package infos
NAMETGZ=${NAMETGZ:-EMBOSS}
BUILD=${BUILD:-1GGD}
ARCH=${ARCH:-i486}
TARGET=${TARGET:-i486}
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMETGZ}
JDK=${JDK:-/usr/lib/jdk1.6.0_11}
CWD=$(pwd)
set -e # Quit if a command returns non-zero
# Sanity checks
if [ $UID -eq 0 ]; then
echo "You should NOT run this script as ROOT!"
exit 1
fi
if [ ! -d $TMP ]; then
echo "$TMP does not exist or is not a directory!"
exit 1
fi
# Compilation flags
case "$ARCH" in
i?86)
CPUOPT="-O2 -march=$ARCH -mtune=i686"
;;
*)
CPUOPT="-O2"
;;
esac
# Get and verify the source archive
if [ ! -r $ARCHIVE ]; then
wget "$WGET"
fi
sha1sum -c $ARCHIVE.sha1
NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1)
# Compile
cd $TMP
echo "Building $ARCHIVE..."
tar xf $CWD/$ARCHIVE
cd $NAME
CFLAGS=$CPUOPT \
CXXFLAGS=$CPUOPT \
./configure \
--prefix=/usr \
--disable-dependency-tracking \
--disable-static \
--with-java=$JDK/include \
--with-javaos=$JDK/include/linux
make -j 3
make install DESTDIR=$PKG
# Tweak JEmboss launch files
RUNJEMBOSS=$PKG/usr/share/EMBOSS/jemboss/runJemboss.sh
JEMBOSSPROPS=$PKG/usr/share/EMBOSS/jemboss/resources/jemboss.properties
sed -i 's|^JEMBOSS_HOME=.|JEMBOSS_HOME=/usr/share/EMBOSS/jemboss|' $RUNJEMBOSS
sed -i 's|/packages/emboss/STABLE|/usr|' $JEMBOSSPROPS
sed -i 's|^embossPath=.*$|embossPath=/usr/bin:/bin|' $JEMBOSSPROPS
chmod 755 $RUNJEMBOSS
ln -sv /usr/share/EMBOSS/jemboss/runJemboss.sh $PKG/usr/bin/jemboss
# Strip binaries
find $PKG | xargs file | grep "ELF 32-bit LSB" | cut -d : -f 1 | \
xargs strip --strip-unneeded 2> /dev/null
# Install the documentation
mkdir -p $PKG/usr/doc/$NAME
install -m 644 \
AUTHORS COMPAT COPYING ChangeLog FAQ KNOWN_BUGS LICENSE NEWS ONEWS \
README THANKS \
$PKG/usr/doc/$NAME
# Copy slack-desc file
mkdir -p $PKG/install
install -m 644 $CWD/slack-desc $PKG/install/slack-desc
# Package the tree
cd $PKG
mkdir -p $OUT
PACKAGING="
chown root:root . -R
/sbin/makepkg -l y -c n $OUT/$NAMETGZ-$VERSION-$ARCH-$BUILD.tgz
rm -rf $PKG
rm -rf $TMP/$NAME
"
if type -p fakeroot ; then
echo "$PACKAGING" | fakeroot
else
su -c "$PACKAGING"
fi

13
ap/EMBOSS/slack-desc

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|-----handy-ruler------------------------------------------------------|
emboss: emboss (European Molecular Biology Open Software Suite)
emboss:
emboss: EMBOSS is a free Open Source software analysis package specially
emboss: developed for the needs of the molecular biology (e.g. EMBnet) user
emboss: community. The software automatically copes with data in a variety
emboss: of formats and even allows transparent retrieval of sequence data
emboss: from the web. Also, as extensive libraries are provided with the
emboss: package, it is a platform to allow other scientists to develop and
emboss: release software in true open source spirit. EMBOSS also integrates
emboss: tools for sequence analysis into a seamless whole. EMBOSS breaks
emboss: the historical trends towards commercial software package.
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