[Bioperl-pipeline] UPDATE action

[jeremyp@sgx3.bmb.uga.edu]

Hi,

The pipeline I am working on right now uses the "UPDATE" action. I found
that when this action is used with later analyses (from the third analysis
onward), it doesn't seem to work (I think this is because the second
analysis jobs are created in the actual InputCreate step). I added
dependency checking code to the section of PipelineManager.pl that builds
new jobs. The code looks like this:


    foreach my $job (@completed_jobs) {
        my ($new_jobs) = &create_new_job($job);
        if(scalar(@{$new_jobs})){
            print STDERR "Creating ".scalar(@{$new_jobs})." jobs\n";
        }
        foreach my $new_job (@{$new_jobs}){
            my $job_depend =
                $ruleAdaptor->check_dependency_by_job($new_job,@rules);
            $new_job->dependency($job_depend);

The last two lines are the addition.

Jeremy