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annotate r_wrapper.sh @ 0:6c1e450b02c3 draft default tip

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planemo upload commit 72cee9103c0ae4acb5794afaed179bea2c729f2c-dirty
author stevecassidy
date Sat, 11 Mar 2017 21:35:38 -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 # Extract first argument
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17 infile=$1; shift
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19 # Ensure the file exists
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20 test -f $infile || fail "R input file '$infile' does not exist"
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22 # Invoke R passing file named by first argument to stdin
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23 R --vanilla --slave --args $* < $infile