Calling external program from R with multiple commands in system

Question

I am new to programming and mainly I am able to do some scripts within R, but for my work I need to call an external program. For this program to work on the ubuntu's terminal I have to first use setenv and then execute the program. Googling I've found the system () and Sys.setenv() functions, but unfortunately I can make it function. This is the code that does work in the ubuntu terminal: ``` $ export PATH=/home/meme/bin:$PATH $ mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp ``` Where the first two arguments are input files, the -o argument is the output directory and the -comp is another parameter for the program to run. The reason that I need to do it in R despite it already works in the terminal is because I need to run the program 1000 times with 1000 different files so I want to make a for loop where the input name changes in every loop and then analyze every output in R. I have already tried to use: ``` Sys.setenv(PATH="/home/meme/bin"); system(ma…

Accepted Answer

Construct the string you want to execute with `paste` and feed that to `system`:

```
for(i in 1:10){
cmd=paste("export FOO=",i," ; echo \"$FOO\" ",sep='')
system(cmd)
}
```

Note the use of `sep=''` to stop `paste` putting spaces in, and back-quoting quote marks in the string to preserve them.

Test before running by using `print(cmd)` instead of `system(cmd)` to make sure you are getting the right command built. Maybe do:

```
if(TESTING){print(cmd)}else{system(cmd)}
```

and set `TESTING=TRUE` or `FALSE` in R before running.

If you are going to be running more than one shell command per `system` call, it might be better to put them all in one shell script file and call that instead, passing parameters from R. Something like:

```
cmd = paste("/home/me/bin/dojob.sh ",i,i+1)
system(cmd)
```

and then `dojob.sh` is a shell script that parses the args. You'll need to learn a bit more shell scripting.

Calling external program from R with multiple commands in system

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