Mercurial > repos > lionelguy > spades
view tools/spades_3_0/r_wrapper.sh @ 8:ff058438080a draft
Version 0.8, supports SPAdes 3.0.0
author | lionelguy |
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date | Wed, 05 Feb 2014 05:19:03 -0500 |
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#!/bin/sh ### Run R providing the R script in $1 as standard input and passing ### the remaining arguments on the command line # Function that writes a message to stderr and exits function fail { echo "$@" >&2 exit 1 } # Ensure R executable is found which R > /dev/null || fail "'R' is required by this tool but was not found on path" # Extract first argument infile=$1; shift # Ensure the file exists test -f $infile || fail "R input file '$infile' does not exist" # Invoke R passing file named by first argument to stdin R --vanilla --slave $* < $infile