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#!/bin/sh
###########################################################################
# Installer for clustal.
#
# Changes:
#
# 25-05-07,Nigel Brown (EMBL): created.
# 08-06-07,Nigel Brown (EMBL): added default link location.
###########################################################################
SAVEPATH=`echo $PATH | tr ':' ' '| sort -u`
PATH=/bin:/usr/bin; export PATH
INSTALLDIR=`pwd`
BINDIR=
SCRIPT=clustalx2
BINARY=clustalx
PROG=`basename $0`
umask 022
cleanup () {
rm -f "$SCRIPT" >/dev/null 2>&1
echo; echo Aborted. 1>&2
exit 1
}
trap cleanup 1 2 3 15
msg () { echo $* 1>&2; }
warn () { echo " + $*" 1>&2; }
error () { echo $PROG: ERROR: $* 1>&2; }
die () { echo $PROG: FATAL: $* 1>&2; exit 1; }
makeLink () {
src="$1"; dest="$2"; file="$3"
[ "$dest" = . ] && return
[ "$src" = "$dest" ] && return
if [ -e "$dest/$file" ]; then
warn "Replacing existing file '$dest/$file'"
rmFile "$dest/$file"
fi
symLink "$src/$file" "$dest/$file"
}
rmFile () {
#warn "Deleting '$1'"
rm -f "$1" >/dev/null 2>&1 || die "Attempt to delete old '$1' failed"
warn "Deleted '$1'"
}
symLink () {
#warn "Symbolic linking '$1' to '$2'"
ln -s "$1" "$2" >/dev/null 2>&1 || die "Attempt to symlink '$1' to '$2' failed"
warn "Symlinked '$1' to '$2'"
}
mkDir () {
mkdir -p "$1" >/dev/null 2>&1
if [ $? -ne 0 ]; then
[ $# -lt 2 ] && die "Can't make directory '$1'"
warn "Can't make directory '$1'"
fi
warn "Created directory '$1'"
}
guessBinDir () {
[ -n "$BINDIR" ] && return #already set/guessed
if [ -e /usr/bin/id ]; then
user=`/usr/bin/id -u`
elif [ -e /bin/id ]; then
user=`/bin/id -u`
elif [ "$USER" = "root" ]; then
user=0
fi
if [ "$user" -eq 0 ]; then
BINDIR=/usr/local/bin
msg "You have administrator/root permissions - good!"
else
BINDIR=$HOME/bin
msg "Note: you must have write permission for the chosen directory."
fi
#echo; msg "The suggested location will be: [$BINDIR]"
unset user
}
pauseAndContinue () {
echo
echo -n "Hit the 'return' or 'enter' key to continue. "
read x
unset x
}
readBinDir () {
dir=
while true; do
echo
echo -n "Choose a directory for the executable [$BINDIR]? "
read dir
echo
if [ -z "$dir" -a -n "$BINDIR" ]; then
dir=$BINDIR
break
fi
if [ "$dir" = "$SCRIPT" ]; then
warn "That name is reserved - please use something else!"
continue
fi
if [ ! -e "$dir" ]; then
mkDir "$dir" nofail
fi
if [ -e "$dir" ]; then
[ -w "$dir" ] && break
warn "Directory '$dir' exists, but is not writeable"
fi
done
BINDIR="$dir"
unset dir
}
checkBinDir () {
if [ -z "$BINDIR" ]; then
die "Directory '$BINDIR' was not specified - aborting"
fi
if [ "$BINDIR" = "$SCRIPT" ]; then
die "That name is reserved - please use something else!"
fi
if [ ! -d "$BINDIR" -a ! -h "$BINDIR" ]; then
mkDir "$BINDIR" nofail
fi
if [ -d "$BINDIR" -o -h "$BINDIR" ]; then
if [ -w "$BINDIR" ]; then
return
fi
die "Directory '$BINDIR' exists, but is not writeable"
fi
die "Directory '$BINDIR' does not exist and could not be created - aborting"
}
makeScript () {
cat<<EOT
#!/bin/sh
###########################################################################
# Version: 1.0
# Generated: `date`
###########################################################################
# Path to the clustal installation directory
export CLU_INSTALL_DIR=$INSTALLDIR
BINARY=$BINARY
###########################################################################
PROG=\`basename \$0\`
# Debugging
#echo CLU_INSTALL_DIR=\$CLU_INSTALL_DIR 1>&2
#echo BINARY=\$BINARY 1>&2
# Is there an executable binary file?
binary=\$CLU_INSTALL_DIR/\$BINARY
if [ ! -f \$binary ]; then
echo "\$PROG: Can't find executable '\$binary'"
exit 1
fi
if [ ! -x \$binary ]; then
echo "\$PROG: Binary '\$binary' is not executable"
exit 1
fi
# Exec the child over this one
exec \$binary \$*
###########################################################################
EOT
}
###########################################################################
if [ ! -f "$BINARY" ]; then
die "You must change into the unpacked clustal directory first!"
fi
rm -f "$SCRIPT" >/dev/null 2>&1
if [ $# -gt 0 ]; then
BINDIR="$1"
else
cat<<EOT
Clustal installer.
A clustal installation consists of two parts: (1) the current directory which
contains all the components that clustal needs to work, and (2) a link to the
clustal executable, which must be placed in a directory on your (or the
users') PATH.
You have already completed step (1) simply by unpacking the archive in its
final destination.
Now complete step (2) by specifying a directory for the executable link. You
can accept the default, or enter a directory from the following list of likely
candidates taken from your PATH.
[$SAVEPATH]
EOT
#pauseAndContinue
guessBinDir
echo; msg "At any time, you may type ^C (ctrl-C) to abort."
readBinDir
fi
checkBinDir
makeScript > "$SCRIPT"
chmod 0755 "$SCRIPT"
makeLink "$INSTALLDIR" "$BINDIR" "$SCRIPT"
cat<<EOT
Location of components: $INSTALLDIR
Location of executable: $BINDIR
Finished.
EOT
exit 0
###########################################################################
|
