ap/clustalw: Added.

ap/clustalw/clustalw.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 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

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

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+d54f3b3fdd3d0fc0317546d6ff91fe9a0db0f51e  clustalw1.83.linux.tar.gz

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: