[Bioperl-pipeline] Re: how to annotate contigs

[Shawn]

Including the list for the benefit of others if you don't mind.

the developer docs are not written yet :)
yes, we have made the BatchSubmission system modular so you should be
able to plug and play as long as you write a module for yours that
basically encapsulates the command used to send jobs off.
If you look under inside Bio::Pipeline::BatchSubmission, you will find
the LSF and PBS implementation. You just need to implement your module
and  1 method,
:
 submit_batch

The  construct_command_line routine is an internal call to the
BatchSubmission module so you can have it if you want.
Its rather lite now, but we use modules in case we want to do more stuff
with the queuing systems. Then you just have to specify inside
PipeConf.pm the name of your module. If u have your system ready, let us
know, and we will be glad to help u incorporate it.


cheers,
shawn




and they 
On Wed, 2002-08-21 at 23:09, Andy Nunberg wrote:
> Thanks,
> I see you write that I must have LFS or PBS, we dont have either and are
> writing our own basic queing system
> will this be a problem??
> Andy
> At 06:53 PM 8/21/2002 +0800, you wrote:
> >There is some install docs on the website
> >
> >http://www.fugu-sg.org/bioperl-pipeline/
> >
> >
> >http://www.fugu-sg.org/bioperl-pipeline/bioperl-pipeline-install.html
> >
> >which might be useful.
> >
> >but this was written eons ago (actually a month ago)... our code dev is
> >changing a lot. so things might look a little different. :)
> >
> >so yes..please send us questions...
> >shawn
> >
> >On Wed, 2002-08-21 at 10:13, Elia Stupka wrote:
> >> > Which documentations were you specifically referring to? I will focus on
> >> > reading those..
> >> 
> >> Ehm.... not much at the moment, but there is some in INSTALL and
> >> database_schema.doc, we will try to add some more today/tomorrow if you
> >> send us questions, we'll include it...
> >> 
> >> Elia
> >> 
> >> ********************************
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> >> 
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> >> 
> >
> 
> *******************************************************************
> Andy Nunberg, Ph.D
> Computational Biologist
> Orion Genomics, LLC 
> (314) 615-6989
> http://www.oriongenomics.com
>