Mercurial > repos > lionelguy > spades
comparison tools/spades_3_0/r_wrapper.sh @ 8:ff058438080a draft
Version 0.8, supports SPAdes 3.0.0
| author | lionelguy |
|---|---|
| date | Wed, 05 Feb 2014 05:19:03 -0500 |
| parents | |
| children |
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| 7:95ddc2380130 | 8:ff058438080a |
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| 1 #!/bin/sh | |
| 2 | |
| 3 ### Run R providing the R script in $1 as standard input and passing | |
| 4 ### the remaining arguments on the command line | |
| 5 | |
| 6 # Function that writes a message to stderr and exits | |
| 7 function fail | |
| 8 { | |
| 9 echo "$@" >&2 | |
| 10 exit 1 | |
| 11 } | |
| 12 | |
| 13 # Ensure R executable is found | |
| 14 which R > /dev/null || fail "'R' is required by this tool but was not found on path" | |
| 15 | |
| 16 # Extract first argument | |
| 17 infile=$1; shift | |
| 18 | |
| 19 # Ensure the file exists | |
| 20 test -f $infile || fail "R input file '$infile' does not exist" | |
| 21 | |
| 22 # Invoke R passing file named by first argument to stdin | |
| 23 R --vanilla --slave $* < $infile |