Re: [galaxy-dev] postgres connection
That worked perfectly! Thanks Nate!
Chris
Galaxy dev:
I'm installing a local galaxy instance (Dec 4, 2012 vintage) and it is
running well under mySQL, but I'm having trouble getting it to work with a
postgres database.
I've done the following to create the db and provide permissions:
$ whoami
galaxy
$ createdb galaxy_prod4
$ psql galaxy_prod4
psql (8.4.13)
Type help for help.
galaxy_prod4=# CREATE ROLE galaxy_prod_role4 WITH PASSWORD 'milkweed';
CREATE ROLE
galaxy_prod4=# GRANT ALL PRIVILEGES ON DATABASE galaxy_prod4 to
galaxy_prod_role4;
GRANT
galaxy_prod4=# ALTER ROLE galaxy_prod_role4 LOGIN;
ALTER ROLE
galaxy_prod4=# \du
List of roles
Role name | Attributes | Member of
---+--+---
galaxy| Superuser| {}
: Create role
: Create DB
galaxy_prod_role | Cannot login | {}
galaxy_prod_role4 | | {}
mydb_role | Cannot login | {}
mydb_user | | {}
postgres | Superuser| {}
: Create role
: Create DB
galaxy_prod4=# \l
List of databases
Name | Owner | Encoding | Collation |Ctype| Access
privileges
--+--+--+-+-+--
galaxy_prod3 | galaxy | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/galaxy
:
galaxy=CTc/galaxy
:
galaxy_prod_role=CTc/galaxy
galaxy_prod4 | galaxy | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/galaxy
:
galaxy=CTc/galaxy
:
galaxy_prod_role4=CTc/galaxy
postgres | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
template0| postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =c/postgres
:
postgres=CTc/postgres
template1| postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =c/postgres
:
postgres=CTc/postgres
(5 rows)
Looks promising, right?
My universe_wsgi.ini has the following entry:
database_connection =
postgres:///galaxy_prod_role4:milkweed@127.0.0.1:5432/galaxy_prod4
Hi Chris,
You're a field off in your URL, try this:
postgres://galaxy_prod_role4:milkweed@127.0.0.1:5432/galaxy_prod4
--nate
and started the application, but it failed with:
OperationalError: (OperationalError) FATAL: database
galaxy_prod_role4:milkweed@127.0.0.1:5432/galaxy_prod4 does not exist
commenting the database_connection line out allows galaxy to start, using
mySQL I presume. Any ideas? This is my first time configuring something like
this.
Thank you!
Chris
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Re: [galaxy-dev] postgres
Hi, thanks for the answer. I have one more question. Is there one main table (in the database), which creates one key for one job and this key is allocated over other tables? Thank you! Best, Christin Am 08.03.2012 16:40, schrieb Björn Grüning: Hi Christin, I would like to clarify whether we have understood something about the database correctly. Is is right that all calculations with galaxy are stored as a link in the database. And the data are stored somewhereelse? Yes, kind of :) Is it possible to store the data only in the database? No and its advisable to do so. Galaxy operates on files and they can be huge. It does not make much sense to store such data in a database. Best, Bjoern For some advice, I am very grateful. Best regards, Christin -- Christin Weinberg Institute for Applied Computer Science (IACS) FH Stralsund - University of Applied Sciences Phone: +49 3831 456948 E-Mail : christin.weinb...@fh-stralsund.de ___ 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/
Re: [galaxy-dev] postgres
Yes, see the table 'job'. You may or may not find this helpful, but here's a big database schema from our wiki: http://wiki.g2.bx.psu.edu/DataModel?action=AttachFiledo=viewtarget=galaxy_schema.png -Dannon On Mar 9, 2012, at 8:00 AM, christin weinberg wrote: Hi, thanks for the answer. I have one more question. Is there one main table (in the database), which creates one key for one job and this key is allocated over other tables? Thank you! Best, Christin Am 08.03.2012 16:40, schrieb Björn Grüning: Hi Christin, I would like to clarify whether we have understood something about the database correctly. Is is right that all calculations with galaxy are stored as a link in the database. And the data are stored somewhereelse? Yes, kind of :) Is it possible to store the data only in the database? No and its advisable to do so. Galaxy operates on files and they can be huge. It does not make much sense to store such data in a database. Best, Bjoern For some advice, I am very grateful. Best regards, Christin -- Christin Weinberg Institute for Applied Computer Science (IACS) FH Stralsund - University of Applied Sciences Phone: +49 3831 456948 E-Mail : christin.weinb...@fh-stralsund.de ___ 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/
Re: [galaxy-dev] postgres
Hi Christin, I would like to clarify whether we have understood something about the database correctly. Is is right that all calculations with galaxy are stored as a link in the database. And the data are stored somewhereelse? Yes, kind of :) Is it possible to store the data only in the database? No and its advisable to do so. Galaxy operates on files and they can be huge. It does not make much sense to store such data in a database. Best, Bjoern For some advice, I am very grateful. Best regards, Christin -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ 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/
