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annotate r_wrapper.sh @ 1:dbcf9bc275e3 draft

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planemo upload commit 063e049d569aeb45e1008cbf044f2dad850eca3d-dirty
author stevecassidy
date Wed, 07 Dec 2016 19:10:51 -0500
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1 #!/bin/sh
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3 ### Run R providing the R script in $1 as standard input and passing
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4 ### the remaining arguments on the command line
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6 # Function that writes a message to stderr and exits
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7 fail()
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8 {
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9 echo "$@" >&2
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10 exit 1
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11 }
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13 # Ensure R executable is found
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14 which R > /dev/null || fail "'R' is required by this tool but was not found on path"
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16 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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18 # Extract first argument
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19 infile=$1; shift
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21 # Ensure the file exists
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22 test -f $infile || fail "R input file '$infile' does not exist"
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24 # Invoke R passing file named by first argument to stdin
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25 # add in the util.R file too containing common functions
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26 cat $DIR/util.R $infile | R --vanilla --slave $*