view tools/spades_2_5/r_wrapper.sh @ 3:d82f18c76309 draft

Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.

#!/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