How do I create a simple script which executes (in Linux) a sequence of commands?

Question

Premise: I know (a bit of) Python.

I'm working on a a R Sweave (R + Latex) document.

To compile and execute it from command line I need to execute the following commands from console:

R CMD Sweaver fn.Rnw
pdflatex fn.tex
okular fn.pdf

Where

fn

varies from time to time (but is the same in all of the instructions).

Since I'm doing this many times, I'd like to make the process automatic and as simple as writing something like:

script <fn>

where fn is the parameters used in the 3 single commands.

I think this is somehow possible in Python or Perl, but I don't know where to begin.

Thanks in advance

Perl is overkill for this. Do it in a shell script. Better yet, learn make, which is the right tool for the job. — Blrfl
– Blrfl, Commented Feb 27, 2014 at 14:31

Rory Hunter · Accepted Answer · 2014-02-27 12:35:44Z

2

Here's an example Perl script (untested):

#!/usr/bin/perl -w

use strict;
use warnings;

my $fn = shift or die "Usage: $0 function_name\n";

# I assume this needs to exist?
-e "$fn.Rnw" or die "$fn.Rnw does not exist.\n";

0 == system( 'R', 'CMD', 'Sweaver', "$fn.Rnw" ) or die "R failed.\n";
0 == system( 'pdflatex ', "$fn.tex" ) or die "pdflatex failed.\n";
0 == system( 'okular ', "$fn.pdf" ) or die "R failed.\n";

exit 0;

Write that to a file, make it executable with chmod +x, and you should be set.

answered Feb 27, 2014 at 12:35

Rory Hunter

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4 Comments

dragonmnl Over a year ago

I tried the script. Error " /usr/lib/R/bin/Rcmd: 62: exec: Sweaver: not found " . I assume 0 == system ('R' , ...) it's different than "R CMD Sweaver fn.Rwn". Can you explain me the system (...) row, please?

Rory Hunter Over a year ago

For e.g. the first system() call, it simply executes the 'R' command and supplies all other values as parameters. It's interesting that you get that error - is "Sweaver" another script or command? Is it a file that you own?

dragonmnl Over a year ago

Sweaver is a library of R statistical software. I assume it's no more than a string which is internally handled to run a program (written according to R syntax)

Pradeep Over a year ago

Try using the full path to the binary R

devnull · Accepted Answer · 2014-02-28 09:55:00Z

1

You could write a script containing:

R CMD Sweaver "$1.Rnw"
pdflatex "$1.tex"
okular "$1.pdf"

If you name it foo.sh, you could invoke it by saying:

sh foo.sh fn

or

bash foo.sh fn

and the shell would use the positional parameter that was passed in order to perform the variable substitution.

answered Feb 28, 2014 at 9:55

devnull

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1 Comment

GC 13 Over a year ago

Yes, shell script will be the way for this. here $1 will be the argument after <file-name>

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