/usr/bin/tophat2 is in tophat 2.1.1+dfsg1-1.
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 | #!/usr/bin/env bash
pbin=""
fl=$(readlink $0)
if [[ -z "$fl" ]]; then
pbin=$(dirname $0)
else
pbin=$(dirname $fl)
fi
export PATH=$pbin:$PATH
$pbin/tophat "$@"
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