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ea6fa6e1e4222bc57e748a4d674d72d9b03475dd EMBOSS-6.0.1.tar.gz |
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#!/bin/bash |
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# Build script for Slackware |
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# Damien Goutte-Gattat "gouttegd" < damien.goutte-gattat at e.ujf-grenoble.fr > |
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# |
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# Redistribution and use of this script, with or without modifications, is |
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# permitted provided that the following conditions are met: |
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# |
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# 1. Redistributions of this script must retain the above copyright |
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# notice, this list of conditions and the following disclaimer. |
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# |
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# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED |
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# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF |
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# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO |
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# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, |
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, |
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# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; |
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# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, |
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# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR |
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# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF |
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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# |
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# Latest EMBOSS sourcecode is available at: |
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# http://emboss.sourceforge.net/ |
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|
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# Source package infos |
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NAMESRC=${NAMESRC:-EMBOSS} |
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VERSION=${VERSION:-6.0.1} |
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ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz} |
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WGET=${WGET:-ftp://emboss.open-bio.org/pub/EMBOSS/$ARCHIVE} |
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|
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# Built package infos |
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NAMETGZ=${NAMETGZ:-EMBOSS} |
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BUILD=${BUILD:-1GGD} |
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ARCH=${ARCH:-i486} |
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TARGET=${TARGET:-i486} |
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|
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# Directories |
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TMP=${TMP:-/tmp} |
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OUT=${OUT:-$TMP/build} |
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PKG=${PKG:-$OUT/$NAMETGZ} |
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JDK=${JDK:-/usr/lib/jdk1.6.0_11} |
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CWD=$(pwd) |
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|
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set -e # Quit if a command returns non-zero |
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|
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# Sanity checks |
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if [ $UID -eq 0 ]; then |
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echo "You should NOT run this script as ROOT!" |
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exit 1 |
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fi |
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if [ ! -d $TMP ]; then |
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echo "$TMP does not exist or is not a directory!" |
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exit 1 |
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fi |
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|
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# Compilation flags |
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case "$ARCH" in |
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i?86) |
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CPUOPT="-O2 -march=$ARCH -mtune=i686" |
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;; |
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*) |
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CPUOPT="-O2" |
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;; |
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esac |
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|
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# Get and verify the source archive |
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if [ ! -r $ARCHIVE ]; then |
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wget "$WGET" |
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fi |
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sha1sum -c $ARCHIVE.sha1 |
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NAME=$(tar ft $ARCHIVE | head -n 1 | cut -d / -f 1) |
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|
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# Compile |
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cd $TMP |
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echo "Building $ARCHIVE..." |
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tar xf $CWD/$ARCHIVE |
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cd $NAME |
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CFLAGS=$CPUOPT \ |
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CXXFLAGS=$CPUOPT \ |
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./configure \ |
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--prefix=/usr \ |
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--disable-dependency-tracking \ |
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--disable-static \ |
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--with-java=$JDK/include \ |
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--with-javaos=$JDK/include/linux |
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make -j 3 |
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make install DESTDIR=$PKG |
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|
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# Tweak JEmboss launch files |
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RUNJEMBOSS=$PKG/usr/share/EMBOSS/jemboss/runJemboss.sh |
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JEMBOSSPROPS=$PKG/usr/share/EMBOSS/jemboss/resources/jemboss.properties |
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sed -i 's|^JEMBOSS_HOME=.|JEMBOSS_HOME=/usr/share/EMBOSS/jemboss|' $RUNJEMBOSS |
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sed -i 's|/packages/emboss/STABLE|/usr|' $JEMBOSSPROPS |
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sed -i 's|^embossPath=.*$|embossPath=/usr/bin:/bin|' $JEMBOSSPROPS |
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chmod 755 $RUNJEMBOSS |
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ln -sv /usr/share/EMBOSS/jemboss/runJemboss.sh $PKG/usr/bin/jemboss |
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|
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# Strip binaries |
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find $PKG | xargs file | grep "ELF 32-bit LSB" | cut -d : -f 1 | \ |
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xargs strip --strip-unneeded 2> /dev/null |
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|
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# Install the documentation |
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mkdir -p $PKG/usr/doc/$NAME |
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install -m 644 \ |
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AUTHORS COMPAT COPYING ChangeLog FAQ KNOWN_BUGS LICENSE NEWS ONEWS \ |
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README THANKS \ |
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$PKG/usr/doc/$NAME |
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|
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# Copy slack-desc file |
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mkdir -p $PKG/install |
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install -m 644 $CWD/slack-desc $PKG/install/slack-desc |
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|
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# Package the tree |
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cd $PKG |
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mkdir -p $OUT |
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PACKAGING=" |
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chown root:root . -R |
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/sbin/makepkg -l y -c n $OUT/$NAMETGZ-$VERSION-$ARCH-$BUILD.tgz |
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rm -rf $PKG |
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rm -rf $TMP/$NAME |
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" |
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if type -p fakeroot ; then |
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echo "$PACKAGING" | fakeroot |
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else |
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su -c "$PACKAGING" |
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fi |
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|
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|-----handy-ruler------------------------------------------------------| |
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emboss: emboss (European Molecular Biology Open Software Suite) |
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emboss: |
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emboss: EMBOSS is a free Open Source software analysis package specially |
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emboss: developed for the needs of the molecular biology (e.g. EMBnet) user |
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emboss: community. The software automatically copes with data in a variety |
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emboss: of formats and even allows transparent retrieval of sequence data |
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emboss: from the web. Also, as extensive libraries are provided with the |
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emboss: package, it is a platform to allow other scientists to develop and |
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emboss: release software in true open source spirit. EMBOSS also integrates |
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emboss: tools for sequence analysis into a seamless whole. EMBOSS breaks |
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emboss: the historical trends towards commercial software package. |
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|
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Reference in new issue