On Tue, Jan 10, 2012 at 11:43 AM, Ryan Golhar

>> 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

       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 =
web1.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally =
web2.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally =
web3.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally =
web4.log:WARNING:galaxy.config:Ryan Golhar - self.set_metadata_externally =

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.
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