/usr/lib/abyss/abyss-bowtie is in abyss 2.0.2-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 | #!/bin/bash
set -eu
case $1 in
--help)
cat <<EOF
Usage: abyss-bowtie [OPTION]... QUERY... TARGET
Align the sequences of the files QUERY to those of the file
TARGET using bowtie.
EOF
exit
;;
--version)
cat <<EOF
abyss-bowtie (ABySS)
Written by Shaun Jackman.
EOF
bowtie --version
exit
;;
esac
# Parse the command line.
bowtie='bowtie -S'
while getopts :j:l:v opt; do
case $opt in
j) bowtie="$bowtie -p$OPTARG";;
l) ;;
v) ;;
\?) echo >&2 "abyss-bowtie: invalid option: $OPTARG"; exit 1;;
esac
done
shift $((OPTIND-1))
query=("$@")
target=${query[${#query[@]}-1]}
unset query[${#query[@]}-1]
index=$target.1.ebwt
# Build the index.
if [ ! -r $index ]; then
echo >&2 "Building the index $index..."
echo >&2 bowtie-build $target $target
bowtie-build $target $target 1>&2
elif [ $index -ot $target ]; then
echo >&2 "The index $index is stale. Rebuilding the index..."
echo >&2 bowtie-build $target $target
bowtie-build $target $target 1>&2
else
echo >&2 "The index $index is up to date."
fi
# Map the reads.
echo >&2 $bowtie $target "${query[@]}"
exec abyss-tofastq -i "${query[@]}" |$bowtie $target -
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