Mercurial > repos > stevecassidy > wrassp
diff r_wrapper.sh @ 1:dbcf9bc275e3 draft
planemo upload commit 063e049d569aeb45e1008cbf044f2dad850eca3d-dirty
| author | stevecassidy |
|---|---|
| date | Wed, 07 Dec 2016 19:10:51 -0500 |
| parents | 6d6dc275b107 |
| children |
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--- a/r_wrapper.sh Mon Aug 15 23:48:20 2016 -0400 +++ b/r_wrapper.sh Wed Dec 07 19:10:51 2016 -0500 @@ -1,6 +1,6 @@ #!/bin/sh -### Run R providing the R script in $1 as standard input and passing +### Run R providing the R script in $1 as standard input and passing ### the remaining arguments on the command line # Function that writes a message to stderr and exits @@ -11,7 +11,9 @@ } # Ensure R executable is found -which R > /dev/null || fail "'R' is required by this tool but was not found on path" +which R > /dev/null || fail "'R' is required by this tool but was not found on path" + +DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" # Extract first argument infile=$1; shift @@ -20,4 +22,5 @@ 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 +# add in the util.R file too containing common functions +cat $DIR/util.R $infile | R --vanilla --slave $*