On Jan 10, 2012, at 10:20 PM, Ryan Golhar wrote:

> On Tue, Jan 10, 2012 at 11:43 AM, Ryan Golhar <ngsbioinformat...@gmail.com> 
> wrote:
> 
> Hi Ryan,
> 
> You could check it in lib/galaxy/config.py, after it's read.  By any chance, 
> are you using galaxy-central vs. galaxy-dist?  It's possible that due to a 
> bug I recently fixed and a certain combination of options, metadata for BAMs 
> would always fail externally and be retried internally, although you should 
> still see log messages indicating that this has happened.
> 
> --nate
> 
> 
> set_metadata_externally is definitely set to True.  I added 1 line to check 
> this:
> 
>        self.set_metadata_externally = string_as_bool( kwargs.get( 
> "set_metadata_externally", "False" ) )
>         self.retry_metadata_internally = string_as_bool( kwargs.get( 
> "retry_metadata_internally", "True" ) )
> +        log.warning( "Ryan Golhar - self.set_metadata_externally = %s" % 
> self.set_metadata_externally )
> 
> and the log files show:
> 
> [galaxy@bic galaxy-dist]$ grep Ryan *.log
> runner0.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally 
> = True
> web0.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally = 
> True
> web1.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally = 
> True
> web2.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally = 
> True
> web3.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally = 
> True
> web4.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally = 
> True
> 
> so I know its being read in correctly. I then proceeded to add the same check 
> in /home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py:
> 
>     #but somewhat trickier (need to recurse up the copied_from tree), for now 
> we'll call set_meta()
> +  log.warning( "Ryan Golhar - self.set_metadata_externally = %s" % 
> self.app.config.set_metadata_externally )
>     if not self.app.config.set_metadata_externally or \
> 
> and it is also set to True:
> [galaxy@bic galaxy-dist]$ grep Ryan *.log
> runner0.log:galaxy.jobs WARNING 2012-01-10 22:17:26,381 Ryan Golhar - 
> self.set_metadata_externally = True
> 
> Clearly something else is going on here.  On my last import of BAM file, even 
> after samtools finished indexing the BAM files, Galaxy never registered those 
> jobs as completed.  So this problem is still there as well.

Thanks for checking these.  So, what does your server log for runner0 look like?

--nate

> 
> 
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