On Jan 9, 2012, at 2:38 PM, Ryan Golhar wrote: > On Fri, Jan 6, 2012 at 12:55 PM, Ryan Golhar <ngsbioinformat...@gmail.com> > wrote: > > This indicates that set_meta is running locally, in the runner process. Can > you make sure there's not a typo in your config? The other possibility is > that external metadata setting failed and it's being retried internally (if > that was true, you'd see messages indicated such in the server log). > > I'm pretty sure there isn't a typo. Here is anything meta related (with > comment lines removed) in my universe_wsgi.*.ini files: > > [galaxy@bic galaxy-dist]$ grep set_meta *.ini > universe_wsgi.ini:set_metadata_externally = True > universe_wsgi.runner.ini:set_metadata_externally = True > universe_wsgi.webapp.ini:set_metadata_externally = True > > [galaxy@bic galaxy-dist]$ grep meta *.ini > universe_wsgi.ini:set_metadata_externally = True > universe_wsgi.runner.ini:set_metadata_externally = True > universe_wsgi.webapp.ini:set_metadata_externally = True > > I just tried it again on some BAM files, and nothing comes up in > /var/log/messages or /var/log/httpd/error_log. Runner0.log also doesn't show > anything except for the upload job being completed. > > > I'm still trying to track this one down. Can I add a debug output string to > show what the value of set_metadata_externally is when its read in? If so, > where would I do this?
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 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
