wget http://search.cpan.org/CPAN/authors/id/D/DL/DLUX/Parallel-ForkManager-0.7.5.tar.gz
and extracted to:
/scratch/misc/parallel/Parallel
[if you have root access to your machine, I would recommend to install this module instead of going for 'use lib'].
Once this is done, all you need is follow the examples and get going :)
For example, I have EST in fasta format files ending with .fas. The genome I am aligning to is NC_010336.fna. For this I can write the following code:
use strict;
use warnings;
use lib '/scratch/misc/parallel/Parallel';
use LWP::Simple;
use Parallel::ForkManager;
system("ls -1 *.fas > list.tmp");
my $command="est2genome";
my $genome="NC_010336.fna";
my @tasks;
open(F,"list.tmp");
while(< F >){chomp;push(@tasks,$_);}
close F;
my $tasksize= @tasks;
print "There are # $tasksize \n";
my $pm = new Parallel::ForkManager($tasksize);
foreach my $task (@tasks) {
$pm->start and next; # do the fork
system("$command $task $genome $task.$genome.out");
$pm->finish;
}
$pm->wait_all_children;
and store is as est2genome_parallel.pl and run it as:
perl est2genome_parallel.pl
above code can be downloaded from http://sharma.animesh.googlepages.com/est2genome_parallel.pl, enjoy :)
... I am also noticing a recent rise in interest for the language 
Posts
