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|
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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 ClustalW sourcecode is available at: |
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# ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ |
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|
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# Source package infos |
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NAMESRC=${NAMESRC:-clustalw} |
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VERSION=${VERSION:-1.83} |
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ARCHIVE=${ARCHIVE:-$NAMESRC$VERSION.linux.tar.gz} |
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WGET=${WGET:-ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/$ARCHIVE} |
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|
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# Built package infos |
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NAMETGZ=${NAMETGZ:-clustalw} |
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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/$NAMETGZ} |
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CWD=$(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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gcc $CPUOPT -c *.c |
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gcc -o clustalw *.o -lm |
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strip --strip-unneeded clustalw |
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|
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# Install |
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mkdir -p $PKG/usr/bin $PKG/usr/doc/$NAMESRC-$VERSION |
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install -m 755 clustalw $PKG/usr/bin |
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install -m 644 \ |
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README_W clustalv.doc clustalw.{doc,ms,new} clustalw_help \ |
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globin.{aln,dnd,pep,ph} gon90.bla matrixseries.gon \ |
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$PKG/usr/doc/$NAMESRC-$VERSION |
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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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d54f3b3fdd3d0fc0317546d6ff91fe9a0db0f51e clustalw1.83.linux.tar.gz |
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|
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|-----handy-ruler------------------------------------------------------| |
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clustalw: clustalw (Multiple sequence alignment program) |
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clustalw: |
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clustalw: ClustalW is a general purpose multiple alignment program for DNA or |
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clustalw: proteins. See Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994). |
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clustalw: CLUSTALW: improving the sensitivity of progressive multiple sequence |
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clustalw: alignment through sequence weighting, positions-specific gap |
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clustalw: penalties and weight matrix choice. Nucleic Acids Research, |
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clustalw: 22:4673-4860. |
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clustalw: |
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clustalw: |
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clustalw: |
Loading…
Reference in new issue