diff tools/spades_3_1_1/r_wrapper.sh @ 10:7d72faef9af0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/spades_3_1_1/r_wrapper.sh	Fri Oct 10 14:40:43 2014 -0400
@@ -0,0 +1,23 @@
+#!/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