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1 #!/bin/sh
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2
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3
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4 #Copied from https://github.com/galaxyproject/galaxy/blob/dev/tools/stats/r_wrapper.sh
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5
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6 ### Run R providing the R script in $1 as standard input and passing
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7 ### the remaining arguments on the command line
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8
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9 # Function that writes a message to stderr and exits
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10 fail()
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11 {
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12 echo "$@" >&2
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13 exit 1
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14 }
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15
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16 # Ensure R executable is found
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17 which R > /dev/null || fail "'R' is required by this tool but was not found on path"
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18
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19 # Extract first argument
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20 rfile=$1
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21 package_file=$2
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22 version_file=$3
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23
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24 # Ensure the file exists
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25 test -f $infile || fail "R input file '$infile' does not exist"
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26
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27 # Invoke R passing file named by first argument to stdin
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28 #Remove --slave for full R output
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29 R --vanilla --slave --args $package_file < $rfile
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30 echo "done"
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