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The existing version fails on symlinks #41

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The existing version fails on symlinks #41

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19 changes: 10 additions & 9 deletions src/tophat2.sh
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
#!/usr/bin/env bash
pbin=""
fl=$(readlink $0)
if [[ -z "$fl" ]]; then
pbin=$(dirname $0)
else
pbin=$(dirname $fl)
fi
export PATH=$pbin:$PATH
$pbin/tophat "$@"
# http://stackoverflow.com/a/246128:
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
export PATH=$DIR:$PATH
$DIR/tophat "$@"