[Bioperl-pipeline] web, restart

[Shawn Hoon]

On Thursday, June 26, 2003, at 07:17  PM, jeremyp at sgx3.bmb.uga.edu 
wrote:

> Hi,
>
> I remember there was some talk about including software to allow for
> running pipelines through a web interface. Has this been done?
>

Uhm, I personally have not been working on this but I think some folks 
at TLL might
be working on this. Aaron you wanna chime in? Should we start some 
discussion on what some issues that need
to be addressed to get this developing seriously?

> Also, is there a way to restart the PipelineManager? That is, if the
> PipelineManager were killed but I wanted the pipeline it was running 
> when
> killed to continue running at a later date, is there a way to do this?
>

Oh definitely, we do it all the time. When you kill the 
PipelineManager, all the job states are
stored in the database. Normally what happens in this scenario is that 
the pipeline user

1) first kills the PipelineManager script
2) does a bkill 0 (for lsf) for his jobs
3) Do whatever fixing one needs and make sure that the inputs and 
output databases are cleaned appropriately
3) The state of the jobs in the job table will have a mix of jobs that 
have status Failed, New, Submitted
     You will need to set the jobs that are in Submitted state back to 
New or Failed. This is because we killed
     the jobs with the bkill before they could write their status back 
to the table. So the PipelineManager upon
    restart will think they are still running (not so clever as to check 
with LSF yet) and only fetch the New|Failed jobs.

   So execute : update job set status="NEW" where status="SUBMITTED"
   in your pipeline database
4) Remove the Pipeline lock file and run PipelineManager again OR
     run PipelineManager with the -f option and it should remove it for 
you.

hope that is clear

cheers,

shawn

	


> Thanks,
> Jeremy
> _______________________________________________
> bioperl-pipeline mailing list
> bioperl-pipeline at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-pipeline
>