[galaxy-dev] Status on importing BAM file into Library does not update

Ryan Golhar ngsbioinformatics at gmail.com
Tue Jan 10 22:20:35 EST 2012


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