Review tools using bash variables (in particular with cp/mv)

[bernt-matthias]

Here cp -r "/" augustus_dir/ will be executed if AUGUSTUS_CONFIG_PATH is not defined. This should happen only if the requirement is not installed, but then we still do not want to copy / :)

We should at least remove the trailing / from $AUGUSTUS_CONFIG_PATH/ and/or add something like

if [ -z "\$AUGUSTUS_CONFIG_PATH" ]; then
    >&2 echo "AUGUSTUS_CONFIG_PATH not set"; 
    exit 1
fi

More candidates for problematic tools: egrep "\\\\\\$" tools/ -r --include "*xml" | grep -v GALAXY | egrep "cp|mv"

I would love to see shellcheck tool_script.sh invoked before tool tests...