Mercurial > repos > brenninc > brenninc_test
changeset 1:18ce5899a17a draft
Uploaded
author | brenninc |
---|---|
date | Tue, 12 Apr 2016 04:14:22 -0400 |
parents | c012ba512834 |
children | c6f96d5d8a75 |
files | r_info.sh |
diffstat | 1 files changed, 30 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_info.sh Tue Apr 12 04:14:22 2016 -0400 @@ -0,0 +1,30 @@ +#!/bin/sh + + +#Copied from https://github.com/galaxyproject/galaxy/blob/dev/tools/stats/r_wrapper.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 +rfile=$1 +package_file=$2 +version_file=$3 + +# 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 +#Remove --slave for full R output +R --vanilla --slave --args $package_file < $rfile +echo "done"