Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

B.5 How to Run Perl Programs

The details of how to run Perl vary
depending on the operating system of your computer. The instructions
that come with the version of Perl you install on your computer
contain all you need to know. I'll just give a short
summary here that will point you in the right direction.

There is a part of the Perl documentation called
perlrun. You can find it at http://www.perl.com/pub/doc/manual/html/pod/perlrunl.
It gives all the options of running Perl, especially on Unix and
Linux; it's complete but not for the beginner.

B.5.1 Running Perl Programs on Unix or Linux

On Unix or Linux, you
usually run Perl programs from the command line. You can run a Perl
program in a file called this_program by typing:

 perl this_program

if you're in the same directory as the program. If
you're not in the same directory, you may have to
give the pathname of the program:

 perl /usr/local/bin/this_program

Usually, you set the first line of this_program to
have the correct pathname for Perl on your system, since different
machines may have installed Perl in different directories. On my
computer, I use the following as the first line of my Perl programs:

#!/usr/bin/perl

You can type which perl to find the pathname where
Perl is installed on your system.

You also usually make the program executable, using the
chmod program:

chmod 755 this_program

If you've set the first line correctly and used
chmod, you can just type the name of the Perl
program to run it. So, if you're in the same
directory as the program, you can type
./this_program or, if the program is in a
directory that's included in your
$PATH or $path variable, you
can type this_program.[1]

[1] $PATH is the variable used for the shells
sh, bash, and
ksh; $path is the variable used
for csh, tcsh, and so
on.

If your Perl program won't run, the error messages
you get from the shell in the command window may be a little
confusing. For instance, the bash shell on my
Linux system gives the error message:

bash: ./my_program: No such file or directory

in two cases: if there really is no program called
my_program in the current directory, or if the
first line of my_program has incorrectly given the
location of Perl. So watch for that, especially when running programs
from CPAN that may have different pathnames for Perl embedded in
their first lines. Also, if you type my_program,
you may get the error message:

bash: my_program: command not found

which means that the operating system can't find the
program. But it's right there in your directory! The
problem is probably that your $PATH or
$path variable doesn't include
the current directory, so that the system isn't even
looking in the current directory for the program. In this case,
change the $PATH or $path
variable (depending on which shell you're using); or
just type ./my_program instead of
my_program.

B.5.2 Running Perl Programs on the Macintosh

On Macs, the recommended way to save Perl
programs is as "droplets." The
MacPerl documentation gives the simple instructions. Basically, you
open the Perl program with the MacPerl application and then choose
Save As and select the Type option Droplet.

You can drag and drop a file onto a droplet in order to use the file
as input (via the @ARGV array).

The new Mac OS X is a Unix system, and on those systems, you have the
option of running Perl programs from the command line as just
described for Unix and Linux systems.

B.5.3 Running Perl Programs on Windows

On Windows computers,
it's usual to associate the filename extension
.pl with Perl programs. This is usually done as
part of the installation process, which modifies the registry
settings to include this file association. You can then launch
this_program.pl by typing
this_program or perl
this_program.pl in an MS-DOS command window.
Windows also has a PATH variable specifying
folders in which the system looks for programs; this is modified by
the Perl installation process to include the path to the folder for
the Perl application, usually c:\perl. If
you're trying to run a Perl program that
isn't installed in a folder known to the
PATH variable, you can type the complete pathname
to the program, e.g., perl
c:\windows\desktop\my_program.pl.