view r_wrapper.sh @ 1:dbcf9bc275e3 draft

planemo upload commit 063e049d569aeb45e1008cbf044f2dad850eca3d-dirty

#!/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"

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

# 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
# add in the util.R file too containing common functions
cat $DIR/util.R $infile | R --vanilla --slave $*