https://github.com/galaxyproject/galaxy
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Tip revision: 438db6b26bd189a91369e88cc792884fbd5ea2c2 authored by Dannon Baker on 23 February 2015, 16:25:23 UTC
Clone .gitignore
Tip revision: 438db6b
r_wrapper.sh
#!/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
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
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