[Solved] Running a R script with in a shell script

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# 1  
Old 01-30-2014
[Solved] Running a R script with in a shell script


I do have an R script named KO.R. Basically reads thousands of files, whose name has a pattern that differs at a portion of the file name, List.txt.


Below is a portion of my Rscript that reads the file.
vi KO.R

Sample =

If I provide the list of the variable portion of the file name like


how could I run this script one by one by reading each of the files and execute the script.

This is what I tried by making a .sh file
while read file


done < /Users/dropBox/List.txt

where List.txt contains the list of the variable portion of the file.

Could you please let me know the best way to excecute this R script with in the .sh executable shell script?
# 2  
Old 01-30-2014
Try this instead:

while read file

    sed 's/\$file/'"$file"'/g' KO.R > KO_NEW.R
    rm KO_NEW.R

done < /Users/dropBox/List.txt

# 3  
Old 01-30-2014
It didn't work
# 4  
Old 01-30-2014
Can you try the following sed command from the command line and check the new .R file to ensure the replacement you wanted has happened:

sed 's/\$file/'"$file"'/g' KO.R > KO_NEW.R

# 5  
Old 01-30-2014
Thanks. I got it working now.

There was a typo on my side.
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