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#!/bin/bash
# Copyright 2013-2020, Derrick Wood <dwood@cs.jhu.edu>
#
# This file is part of the Kraken 2 taxonomic sequence classification system.
set -e
VERSION="2.1.1"
if [ -z "$1" ] || [ -n "$2" ]
then
echo "Usage: $(basename $0) KRAKEN2_DIR"
exit 64
fi
if [ "$1" = "KRAKEN2_DIR" ]
then
echo "Please replace \"KRAKEN2_DIR\" with the name of the directory"
echo "that you want to install Kraken 2 in."
exit 1
fi
# Perl cmd used to canonicalize dirname - "readlink -f" doesn't work
# on OS X.
export KRAKEN2_DIR=$(perl -MCwd=abs_path -le 'print abs_path(shift)' "$1")
mkdir -p "$KRAKEN2_DIR"
make -C src install
for file in scripts/*
do
perl -pl -e 'BEGIN { while (@ARGV) { $_ = shift; ($k,$v) = split /=/, $_, 2; $H{$k} = $v } }'\
-e 's/#####=(\w+)=#####/$H{$1}/g' \
"KRAKEN2_DIR=/usr/lib/kraken2" "VERSION=$VERSION" \
< "$file" > "$KRAKEN2_DIR/$(basename $file)"
if [ -x "$file" ]
then
chmod +x "$KRAKEN2_DIR/$(basename $file)"
fi
done
echo
echo "Kraken 2 installation complete."
echo
echo "To make things easier for you, you may want to copy/symlink the following"
echo "files into a directory in your PATH:"
for file in $KRAKEN2_DIR/kraken2*
do
if [ -x "$file" ]
then
echo " $file"
fi
done
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