ap/EMBOSS: Added.

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

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+ea6fa6e1e4222bc57e748a4d674d72d9b03475dd  EMBOSS-6.0.1.tar.gz

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

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.
+