[Bioperl-pipeline] creating jobs, job_setup
Alexandre Dehne
dehneg at labri.fr
Tue Feb 10 12:31:42 EST 2004
Hi,
First, I would like to congratulate the Biopipe team for having created such a useful tool.
The context :
For several reasons (some goods and some not so good), some of my runnables take nothing in input and return nothing.
The problem :
This type of runnables does not match the biopipe "spirit", so it is a problem to create jobs for these runnables via the "create_job" function which needs a array input.
The "temporary" unrighteous solution :
I have created an InputCreate module named setup_nothing which creates a void input like the following :
my @input=$self->create_input("nothing",'',"infile");
my $job = $self->create_job($next_anal,\@input);
$self->dbadaptor->get_JobAdaptor->store($job);
This way, I launch one job on my analysis as well as on the following ones by placing "<action>COPY_ID_FILE</action>" in their respective rules in the XML file.
The questions :
Is there a clean way to create jobs without any input (a just_do_it function ?) ?
Perhaps the <job_setup> mark in the XML file ?
Also, could someone tell me more about this <job_setup> mark ???
Thank you in advance
Alexandre
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