Browse Source

ap/clustalw: Added.

slackware-14.2
Damien Goutte-Gattat 13 years ago
parent
commit
a0d3e57acf
  1. 106
      ap/clustalw/clustalw.SlackBuild
  2. 1
      ap/clustalw/clustalw1.83.linux.tar.gz.sha1
  3. 12
      ap/clustalw/slack-desc

106
ap/clustalw/clustalw.SlackBuild

@ -0,0 +1,106 @@
#!/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 ClustalW sourcecode is available at:
# ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
# Source package infos
NAMESRC=${NAMESRC:-clustalw}
VERSION=${VERSION:-1.83}
ARCHIVE=${ARCHIVE:-$NAMESRC$VERSION.linux.tar.gz}
WGET=${WGET:-ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/$ARCHIVE}
# Built package infos
NAMETGZ=${NAMETGZ:-clustalw}
BUILD=${BUILD:-1GGD}
ARCH=${ARCH:-i486}
TARGET=${TARGET:-i486}
# Directories
TMP=${TMP:-/tmp}
OUT=${OUT:-$TMP/build}
PKG=${PKG:-$OUT/$NAMETGZ}
CWD=$(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
gcc $CPUOPT -c *.c
gcc -o clustalw *.o -lm
strip --strip-unneeded clustalw
# Install
mkdir -p $PKG/usr/bin $PKG/usr/doc/$NAMESRC-$VERSION
install -m 755 clustalw $PKG/usr/bin
install -m 644 \
README_W clustalv.doc clustalw.{doc,ms,new} clustalw_help \
globin.{aln,dnd,pep,ph} gon90.bla matrixseries.gon \
$PKG/usr/doc/$NAMESRC-$VERSION
# 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

1
ap/clustalw/clustalw1.83.linux.tar.gz.sha1

@ -0,0 +1 @@
d54f3b3fdd3d0fc0317546d6ff91fe9a0db0f51e clustalw1.83.linux.tar.gz

12
ap/clustalw/slack-desc

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|-----handy-ruler------------------------------------------------------|
clustalw: clustalw (Multiple sequence alignment program)
clustalw:
clustalw: ClustalW is a general purpose multiple alignment program for DNA or
clustalw: proteins. See Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994).
clustalw: CLUSTALW: improving the sensitivity of progressive multiple sequence
clustalw: alignment through sequence weighting, positions-specific gap
clustalw: penalties and weight matrix choice. Nucleic Acids Research,
clustalw: 22:4673-4860.
clustalw:
clustalw:
clustalw:
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