Hi Dannon,
two days of going crazy have an end. It works, tanks!
-Christian
Dannon Baker wrote:
Christian,
This is an issue with postgres9 and our JSONType custom datatype. I have a
ticket open that you can follow if you'd like to be notified of the resolution.
Here's the link:
https://bitbucket.org/galaxy/galaxy-central/issue/434/error-listing-and-running-workflows
-Dannon
On Feb 16, 2011, at 10:54 AM, Christian Dreischer wrote:
Nate Coraor wrote:
Christian Dreischer wrote:
Hello community,
I'm new to Galaxy and are currently trying to install a new instance on a
debian system.
So far I installed postgres and created a user and a database for galaxy.
In the universe_wsgi.ini file I did the recommended changes and set this entry:
database_connection = postgres:///galaxydb?host=/var/run/postgresql
for the connection to postgres.
For test purposes I uploaded the test file from
http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt.
After uploading the file I get a warning that "required metadata values are
missing". Auto-detect doesn't help. Since it all works fine with sqlite, I assume an
incorrect configuration of the postgres user and|or a missing or false entries in
pg_hba.conf or universe_wsgi.ini.
Hi Christian,
Are there any messages related to metadata in the Galaxy server output
(paster.log or console output)?
--nate
Thanks in advance for any suggestions
Christian
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Hi Nate,
these are the entries concerning metadata in the paster.log:
set_metadata.sh ./database/files ./database/tmp
/extern1_512gb/cdreischer/galaxy-dist datatypes_conf.xml None
database/tmp/metadata_in_HistoryDatasetAssociation_4_7q40pL,database/tmp/metadata_kwds_HistoryDatasetAssociation_4_sQy7Sw,database/tmp/metadata_out_HistoryDatasetAssociation_4_4PrDHi,database/tmp/metadata_results_HistoryDatasetAssociation_4_HhKfrH,,database/tmp/metadata_override_HistoryDatasetAssociation_4_l9bvY5
galaxy.jobs.runners.local DEBUG 2011-02-16 16:19:56,486 execution finished:
/extern1_512gb/cdreischer/galaxy-dist/set_metadata.sh ./database/files
./database/tmp /extern1_512gb/cdreischer/galaxy-dist datatypes_conf.xml None
database/tmp/metadata_in_HistoryDatasetAssociation_4_7q40pL,database/tmp/metadata_kwds_HistoryDatasetAssociation_4_sQy7Sw,database/tmp/metadata_out_HistoryDatasetAssociation_4_4PrDHi,database/tmp/metadata_results_HistoryDatasetAssociation_4_HhKfrH,,database/tmp/metadata_override_HistoryDatasetAssociation_4_l9bvY5
galaxy.datatypes.metadata DEBUG 2011-02-16 16:19:56,931 loading metadata from
file for: HistoryDatasetAssociation 4
galaxy.jobs DEBUG 2011-02-16 16:19:57,019 job 8 ended
galaxy.datatypes.metadata DEBUG 2011-02-16 16:19:57,020 Cleaning up external
metadata files
I also set
"set_metadata_externally" and "retry_metadata_internally" to True,
unfortunately without any change.
-Christian
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